Starting phenix.real_space_refine on Tue Aug 26 22:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r87_53806/08_2025/9r87_53806.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r87_53806/08_2025/9r87_53806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r87_53806/08_2025/9r87_53806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r87_53806/08_2025/9r87_53806.map" model { file = "/net/cci-nas-00/data/ceres_data/9r87_53806/08_2025/9r87_53806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r87_53806/08_2025/9r87_53806.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 13117 2.51 5 N 3419 2.21 5 O 3991 1.98 5 H 21814 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42419 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "A1" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A2" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A3" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "A4" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Ar" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "As" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "At" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Au" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Av" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Aw" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Ax" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Ay" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "Az" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1048 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "B" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "C" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "D" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "E" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "F" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "G" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "I" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "J" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "K" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "L" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "M" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "O" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Q" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "S" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "U" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "V" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "W" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "X" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "Y" Number of atoms: 1297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1297 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Z" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 918 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 5.95, per 1000 atoms: 0.14 Number of scatterers: 42419 At special positions: 0 Unit cell: (198.9, 198.9, 67.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 O 3991 8.00 N 3419 7.00 C 13117 6.00 H 21814 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 976.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 1 sheets defined 83.7% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 769 through 802 removed outlier: 3.582A pdb=" N ALA A 773 " --> pdb=" O GLU A 769 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 802 " --> pdb=" O MET A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 824 removed outlier: 3.681A pdb=" N ARG A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Proline residue: A 815 - end of helix removed outlier: 3.519A pdb=" N GLN A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 848 Processing helix chain 'A1' and resid 770 through 803 Processing helix chain 'A1' and resid 803 through 824 removed outlier: 3.621A pdb=" N ALAA1 813 " --> pdb=" O ASPA1 809 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLYA1 814 " --> pdb=" O LEUA1 810 " (cutoff:3.500A) Proline residue: A1 815 - end of helix Processing helix chain 'A2' and resid 770 through 803 Processing helix chain 'A2' and resid 803 through 824 removed outlier: 3.845A pdb=" N GLYA2 814 " --> pdb=" O LEUA2 810 " (cutoff:3.500A) Proline residue: A2 815 - end of helix removed outlier: 3.712A pdb=" N GLNA2 818 " --> pdb=" O GLYA2 814 " (cutoff:3.500A) Processing helix chain 'A3' and resid 770 through 803 Processing helix chain 'A3' and resid 803 through 824 removed outlier: 3.998A pdb=" N GLYA3 814 " --> pdb=" O LEUA3 810 " (cutoff:3.500A) Proline residue: A3 815 - end of helix Processing helix chain 'A4' and resid 770 through 803 Processing helix chain 'A4' and resid 803 through 824 removed outlier: 3.514A pdb=" N ALAA4 813 " --> pdb=" O ASPA4 809 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLYA4 814 " --> pdb=" O LEUA4 810 " (cutoff:3.500A) Proline residue: A4 815 - end of helix Processing helix chain 'Ar' and resid 770 through 803 Processing helix chain 'Ar' and resid 803 through 824 removed outlier: 3.872A pdb=" N GLYAr 814 " --> pdb=" O LEUAr 810 " (cutoff:3.500A) Proline residue: Ar 815 - end of helix Processing helix chain 'As' and resid 770 through 803 Processing helix chain 'As' and resid 803 through 824 removed outlier: 3.684A pdb=" N ALAAs 813 " --> pdb=" O ASPAs 809 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLYAs 814 " --> pdb=" O LEUAs 810 " (cutoff:3.500A) Proline residue: As 815 - end of helix Processing helix chain 'At' and resid 770 through 803 Processing helix chain 'At' and resid 803 through 824 removed outlier: 3.523A pdb=" N ALAAt 813 " --> pdb=" O ASPAt 809 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLYAt 814 " --> pdb=" O LEUAt 810 " (cutoff:3.500A) Proline residue: At 815 - end of helix Processing helix chain 'Au' and resid 770 through 803 Processing helix chain 'Au' and resid 803 through 824 removed outlier: 3.593A pdb=" N ALAAu 813 " --> pdb=" O ASPAu 809 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLYAu 814 " --> pdb=" O LEUAu 810 " (cutoff:3.500A) Proline residue: Au 815 - end of helix Processing helix chain 'Av' and resid 770 through 803 Processing helix chain 'Av' and resid 803 through 812 Processing helix chain 'Av' and resid 812 through 824 Processing helix chain 'Aw' and resid 770 through 802 Processing helix chain 'Aw' and resid 803 through 824 removed outlier: 3.572A pdb=" N ALAAw 813 " --> pdb=" O ASPAw 809 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLYAw 814 " --> pdb=" O LEUAw 810 " (cutoff:3.500A) Proline residue: Aw 815 - end of helix Processing helix chain 'Ax' and resid 770 through 803 Processing helix chain 'Ax' and resid 803 through 824 removed outlier: 3.976A pdb=" N GLYAx 814 " --> pdb=" O LEUAx 810 " (cutoff:3.500A) Proline residue: Ax 815 - end of helix Processing helix chain 'Ay' and resid 770 through 803 Processing helix chain 'Ay' and resid 803 through 824 removed outlier: 4.053A pdb=" N GLYAy 814 " --> pdb=" O LEUAy 810 " (cutoff:3.500A) Proline residue: Ay 815 - end of helix Processing helix chain 'Az' and resid 770 through 803 Processing helix chain 'Az' and resid 803 through 824 removed outlier: 3.928A pdb=" N GLYAz 814 " --> pdb=" O LEUAz 810 " (cutoff:3.500A) Proline residue: Az 815 - end of helix Processing helix chain 'B' and resid 770 through 802 removed outlier: 3.809A pdb=" N GLU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 825 Processing helix chain 'C' and resid 770 through 802 Processing helix chain 'C' and resid 803 through 826 removed outlier: 3.647A pdb=" N ALA C 811 " --> pdb=" O ILE C 807 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY C 814 " --> pdb=" O LEU C 810 " (cutoff:3.500A) Proline residue: C 815 - end of helix removed outlier: 3.644A pdb=" N GLN C 818 " --> pdb=" O GLY C 814 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 822 " --> pdb=" O GLN C 818 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 848 Processing helix chain 'D' and resid 770 through 802 removed outlier: 3.592A pdb=" N GLU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 790 " --> pdb=" O GLN D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 825 removed outlier: 4.405A pdb=" N MET D 817 " --> pdb=" O ALA D 813 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 802 Processing helix chain 'E' and resid 803 through 826 removed outlier: 3.657A pdb=" N ALA E 811 " --> pdb=" O ILE E 807 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Proline residue: E 815 - end of helix removed outlier: 3.604A pdb=" N GLN E 818 " --> pdb=" O GLY E 814 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU E 822 " --> pdb=" O GLN E 818 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 825 " --> pdb=" O LEU E 821 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 826 " --> pdb=" O LEU E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 848 Processing helix chain 'F' and resid 770 through 802 removed outlier: 3.678A pdb=" N GLU F 778 " --> pdb=" O ARG F 774 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 790 " --> pdb=" O GLN F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 803 through 807 Processing helix chain 'F' and resid 810 through 812 No H-bonds generated for 'chain 'F' and resid 810 through 812' Processing helix chain 'F' and resid 813 through 825 removed outlier: 4.379A pdb=" N MET F 817 " --> pdb=" O ALA F 813 " (cutoff:3.500A) Processing helix chain 'G' and resid 770 through 802 Processing helix chain 'G' and resid 803 through 824 removed outlier: 3.627A pdb=" N ILE G 807 " --> pdb=" O GLY G 803 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY G 814 " --> pdb=" O LEU G 810 " (cutoff:3.500A) Proline residue: G 815 - end of helix removed outlier: 3.569A pdb=" N GLN G 818 " --> pdb=" O GLY G 814 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU G 822 " --> pdb=" O GLN G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 840 through 848 Processing helix chain 'H' and resid 770 through 802 removed outlier: 3.627A pdb=" N GLU H 778 " --> pdb=" O ARG H 774 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL H 790 " --> pdb=" O GLN H 786 " (cutoff:3.500A) Processing helix chain 'H' and resid 803 through 807 Processing helix chain 'H' and resid 814 through 825 Processing helix chain 'I' and resid 770 through 802 Processing helix chain 'I' and resid 803 through 826 removed outlier: 3.523A pdb=" N ALA I 811 " --> pdb=" O ILE I 807 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY I 814 " --> pdb=" O LEU I 810 " (cutoff:3.500A) Proline residue: I 815 - end of helix removed outlier: 4.082A pdb=" N LEU I 822 " --> pdb=" O GLN I 818 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU I 825 " --> pdb=" O LEU I 821 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY I 826 " --> pdb=" O LEU I 822 " (cutoff:3.500A) Processing helix chain 'I' and resid 840 through 848 Processing helix chain 'J' and resid 770 through 803 removed outlier: 3.613A pdb=" N GLU J 778 " --> pdb=" O ARG J 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU J 789 " --> pdb=" O GLN J 785 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL J 790 " --> pdb=" O GLN J 786 " (cutoff:3.500A) Processing helix chain 'J' and resid 804 through 809 removed outlier: 3.749A pdb=" N ARG J 808 " --> pdb=" O PRO J 804 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP J 809 " --> pdb=" O SER J 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 804 through 809' Processing helix chain 'J' and resid 814 through 825 Processing helix chain 'K' and resid 770 through 802 removed outlier: 3.612A pdb=" N ILE K 802 " --> pdb=" O MET K 798 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 826 removed outlier: 3.520A pdb=" N ALA K 811 " --> pdb=" O ILE K 807 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY K 814 " --> pdb=" O LEU K 810 " (cutoff:3.500A) Proline residue: K 815 - end of helix removed outlier: 3.581A pdb=" N GLN K 818 " --> pdb=" O GLY K 814 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU K 822 " --> pdb=" O GLN K 818 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU K 825 " --> pdb=" O LEU K 821 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY K 826 " --> pdb=" O LEU K 822 " (cutoff:3.500A) Processing helix chain 'K' and resid 840 through 848 Processing helix chain 'L' and resid 770 through 803 removed outlier: 3.565A pdb=" N GLU L 778 " --> pdb=" O ARG L 774 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL L 790 " --> pdb=" O GLN L 786 " (cutoff:3.500A) Processing helix chain 'L' and resid 804 through 807 Processing helix chain 'L' and resid 810 through 813 Processing helix chain 'L' and resid 814 through 825 removed outlier: 3.539A pdb=" N LYS L 820 " --> pdb=" O GLU L 816 " (cutoff:3.500A) Processing helix chain 'M' and resid 770 through 802 removed outlier: 3.728A pdb=" N ILE M 802 " --> pdb=" O MET M 798 " (cutoff:3.500A) Processing helix chain 'M' and resid 803 through 826 removed outlier: 4.368A pdb=" N GLY M 814 " --> pdb=" O LEU M 810 " (cutoff:3.500A) Proline residue: M 815 - end of helix removed outlier: 3.567A pdb=" N GLN M 818 " --> pdb=" O GLY M 814 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU M 822 " --> pdb=" O GLN M 818 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU M 825 " --> pdb=" O LEU M 821 " (cutoff:3.500A) Processing helix chain 'M' and resid 840 through 848 Processing helix chain 'N' and resid 770 through 803 removed outlier: 3.580A pdb=" N GLU N 778 " --> pdb=" O ARG N 774 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU N 789 " --> pdb=" O GLN N 785 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL N 790 " --> pdb=" O GLN N 786 " (cutoff:3.500A) Processing helix chain 'N' and resid 804 through 807 Processing helix chain 'N' and resid 810 through 813 Processing helix chain 'N' and resid 814 through 825 Processing helix chain 'O' and resid 770 through 802 removed outlier: 3.838A pdb=" N ILE O 802 " --> pdb=" O MET O 798 " (cutoff:3.500A) Processing helix chain 'O' and resid 803 through 826 removed outlier: 3.582A pdb=" N ILE O 807 " --> pdb=" O GLY O 803 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY O 814 " --> pdb=" O LEU O 810 " (cutoff:3.500A) Proline residue: O 815 - end of helix removed outlier: 3.560A pdb=" N GLN O 818 " --> pdb=" O GLY O 814 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU O 822 " --> pdb=" O GLN O 818 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU O 825 " --> pdb=" O LEU O 821 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY O 826 " --> pdb=" O LEU O 822 " (cutoff:3.500A) Processing helix chain 'O' and resid 840 through 848 Processing helix chain 'P' and resid 770 through 803 removed outlier: 3.571A pdb=" N GLU P 778 " --> pdb=" O ARG P 774 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL P 790 " --> pdb=" O GLN P 786 " (cutoff:3.500A) Processing helix chain 'P' and resid 804 through 807 Processing helix chain 'P' and resid 810 through 813 Processing helix chain 'P' and resid 814 through 825 Processing helix chain 'Q' and resid 770 through 802 removed outlier: 3.688A pdb=" N ILE Q 802 " --> pdb=" O MET Q 798 " (cutoff:3.500A) Processing helix chain 'Q' and resid 803 through 826 removed outlier: 3.522A pdb=" N ALA Q 811 " --> pdb=" O ILE Q 807 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY Q 814 " --> pdb=" O LEU Q 810 " (cutoff:3.500A) Proline residue: Q 815 - end of helix removed outlier: 3.610A pdb=" N GLN Q 818 " --> pdb=" O GLY Q 814 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU Q 822 " --> pdb=" O GLN Q 818 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU Q 825 " --> pdb=" O LEU Q 821 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY Q 826 " --> pdb=" O LEU Q 822 " (cutoff:3.500A) Processing helix chain 'Q' and resid 840 through 848 Processing helix chain 'R' and resid 770 through 803 removed outlier: 3.599A pdb=" N GLU R 778 " --> pdb=" O ARG R 774 " (cutoff:3.500A) Processing helix chain 'R' and resid 804 through 807 Processing helix chain 'R' and resid 810 through 813 Processing helix chain 'R' and resid 814 through 825 removed outlier: 3.517A pdb=" N LYS R 820 " --> pdb=" O GLU R 816 " (cutoff:3.500A) Processing helix chain 'S' and resid 770 through 802 removed outlier: 3.800A pdb=" N ILE S 802 " --> pdb=" O MET S 798 " (cutoff:3.500A) Processing helix chain 'S' and resid 803 through 826 removed outlier: 3.754A pdb=" N ILE S 807 " --> pdb=" O GLY S 803 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA S 811 " --> pdb=" O ILE S 807 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY S 814 " --> pdb=" O LEU S 810 " (cutoff:3.500A) Proline residue: S 815 - end of helix removed outlier: 3.625A pdb=" N GLN S 818 " --> pdb=" O GLY S 814 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU S 822 " --> pdb=" O GLN S 818 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU S 825 " --> pdb=" O LEU S 821 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY S 826 " --> pdb=" O LEU S 822 " (cutoff:3.500A) Processing helix chain 'S' and resid 840 through 848 Processing helix chain 'T' and resid 770 through 803 removed outlier: 3.519A pdb=" N GLU T 778 " --> pdb=" O ARG T 774 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU T 789 " --> pdb=" O GLN T 785 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL T 790 " --> pdb=" O GLN T 786 " (cutoff:3.500A) Processing helix chain 'T' and resid 804 through 807 Processing helix chain 'T' and resid 810 through 813 Processing helix chain 'T' and resid 814 through 825 Processing helix chain 'U' and resid 770 through 802 removed outlier: 4.002A pdb=" N ILE U 802 " --> pdb=" O MET U 798 " (cutoff:3.500A) Processing helix chain 'U' and resid 803 through 826 removed outlier: 3.592A pdb=" N ILE U 807 " --> pdb=" O GLY U 803 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA U 811 " --> pdb=" O ILE U 807 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY U 814 " --> pdb=" O LEU U 810 " (cutoff:3.500A) Proline residue: U 815 - end of helix removed outlier: 3.889A pdb=" N LEU U 822 " --> pdb=" O GLN U 818 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU U 825 " --> pdb=" O LEU U 821 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY U 826 " --> pdb=" O LEU U 822 " (cutoff:3.500A) Processing helix chain 'U' and resid 840 through 848 Processing helix chain 'V' and resid 770 through 803 removed outlier: 3.570A pdb=" N GLU V 778 " --> pdb=" O ARG V 774 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU V 789 " --> pdb=" O GLN V 785 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL V 790 " --> pdb=" O GLN V 786 " (cutoff:3.500A) Processing helix chain 'V' and resid 804 through 807 Processing helix chain 'V' and resid 810 through 813 Processing helix chain 'V' and resid 814 through 825 Processing helix chain 'W' and resid 770 through 802 removed outlier: 3.669A pdb=" N ILE W 802 " --> pdb=" O MET W 798 " (cutoff:3.500A) Processing helix chain 'W' and resid 803 through 826 removed outlier: 3.538A pdb=" N ILE W 807 " --> pdb=" O GLY W 803 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLY W 814 " --> pdb=" O LEU W 810 " (cutoff:3.500A) Proline residue: W 815 - end of helix removed outlier: 3.732A pdb=" N GLN W 818 " --> pdb=" O GLY W 814 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU W 822 " --> pdb=" O GLN W 818 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU W 825 " --> pdb=" O LEU W 821 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY W 826 " --> pdb=" O LEU W 822 " (cutoff:3.500A) Processing helix chain 'W' and resid 840 through 848 Processing helix chain 'X' and resid 770 through 803 removed outlier: 3.517A pdb=" N GLU X 778 " --> pdb=" O ARG X 774 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL X 790 " --> pdb=" O GLN X 786 " (cutoff:3.500A) Processing helix chain 'X' and resid 804 through 807 Processing helix chain 'X' and resid 810 through 813 Processing helix chain 'X' and resid 814 through 825 Processing helix chain 'Y' and resid 770 through 802 removed outlier: 3.664A pdb=" N ILE Y 802 " --> pdb=" O MET Y 798 " (cutoff:3.500A) Processing helix chain 'Y' and resid 803 through 824 removed outlier: 3.759A pdb=" N ILE Y 807 " --> pdb=" O GLY Y 803 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY Y 814 " --> pdb=" O LEU Y 810 " (cutoff:3.500A) Proline residue: Y 815 - end of helix removed outlier: 3.660A pdb=" N GLN Y 818 " --> pdb=" O GLY Y 814 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU Y 822 " --> pdb=" O GLN Y 818 " (cutoff:3.500A) Processing helix chain 'Y' and resid 840 through 848 Processing helix chain 'Z' and resid 770 through 803 removed outlier: 3.666A pdb=" N GLU Z 778 " --> pdb=" O ARG Z 774 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL Z 790 " --> pdb=" O GLN Z 786 " (cutoff:3.500A) Processing helix chain 'Z' and resid 804 through 807 Processing helix chain 'Z' and resid 810 through 813 Processing helix chain 'Z' and resid 814 through 825 Processing sheet with id=AA1, first strand: chain 'A' and resid 829 through 834 removed outlier: 6.476A pdb=" N THR A 830 " --> pdb=" O ILEAr 832 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SERAr 829 " --> pdb=" O SER Y 829 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SERA4 829 " --> pdb=" O SER W 829 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SERA3 829 " --> pdb=" O SER U 829 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SERA2 829 " --> pdb=" O LEU S 831 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N THR S 833 " --> pdb=" O SERA2 829 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEUA2 831 " --> pdb=" O THR S 833 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SERA1 829 " --> pdb=" O LEU Q 831 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR Q 833 " --> pdb=" O SERA1 829 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEUA1 831 " --> pdb=" O THR Q 833 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SERAz 829 " --> pdb=" O SER O 829 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SERAy 829 " --> pdb=" O LEU M 831 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR M 833 " --> pdb=" O SERAy 829 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEUAy 831 " --> pdb=" O THR M 833 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SERAx 829 " --> pdb=" O SER K 829 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SERAw 829 " --> pdb=" O SER I 829 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SERAv 829 " --> pdb=" O LEU G 831 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N THR G 833 " --> pdb=" O SERAv 829 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEUAv 831 " --> pdb=" O THR G 833 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SERAu 829 " --> pdb=" O SER E 829 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEUAt 827 " --> pdb=" O SER C 829 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU C 831 " --> pdb=" O LEUAt 827 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N SERAt 829 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR C 833 " --> pdb=" O SERAt 829 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEUAt 831 " --> pdb=" O THR C 833 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER A 829 " --> pdb=" O SERAs 829 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N LEUAs 831 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 831 " --> pdb=" O LEUAs 831 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THRAs 833 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 833 " --> pdb=" O THRAs 833 " (cutoff:3.500A) 1687 hydrogen bonds defined for protein. 4998 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: 9.26 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4524 1.04 - 1.23: 20136 1.23 - 1.43: 4928 1.43 - 1.63: 12844 1.63 - 1.82: 156 Bond restraints: 42588 Sorted by residual: bond pdb=" N ALA I 773 " pdb=" H ALA I 773 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" NH2 ARG I 808 " pdb="HH22 ARG I 808 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 GLN L 823 " pdb="HE21 GLN L 823 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE2 TYRAv 772 " pdb=" HE2 TYRAv 772 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 GLN N 797 " pdb="HE22 GLN N 797 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 42583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 59142 1.92 - 3.84: 13350 3.84 - 5.75: 3336 5.75 - 7.67: 1921 7.67 - 9.59: 134 Bond angle restraints: 77883 Sorted by residual: angle pdb=" CA ASP Z 809 " pdb=" CB ASP Z 809 " pdb=" CG ASP Z 809 " ideal model delta sigma weight residual 112.60 118.10 -5.50 1.00e+00 1.00e+00 3.02e+01 angle pdb=" CA ASP F 809 " pdb=" CB ASP F 809 " pdb=" CG ASP F 809 " ideal model delta sigma weight residual 112.60 117.85 -5.25 1.00e+00 1.00e+00 2.75e+01 angle pdb=" CA ASP B 809 " pdb=" CB ASP B 809 " pdb=" CG ASP B 809 " ideal model delta sigma weight residual 112.60 117.72 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" C GLY H 803 " pdb=" N PRO H 804 " pdb=" CA PRO H 804 " ideal model delta sigma weight residual 119.84 126.13 -6.29 1.25e+00 6.40e-01 2.53e+01 angle pdb=" CA ASP L 809 " pdb=" CB ASP L 809 " pdb=" CG ASP L 809 " ideal model delta sigma weight residual 112.60 117.63 -5.03 1.00e+00 1.00e+00 2.53e+01 ... (remaining 77878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 17709 17.98 - 35.96: 997 35.96 - 53.95: 444 53.95 - 71.93: 390 71.93 - 89.91: 51 Dihedral angle restraints: 19591 sinusoidal: 11336 harmonic: 8255 Sorted by residual: dihedral pdb=" C ASP R 809 " pdb=" N ASP R 809 " pdb=" CA ASP R 809 " pdb=" CB ASP R 809 " ideal model delta harmonic sigma weight residual -122.60 -138.38 15.78 0 2.50e+00 1.60e-01 3.99e+01 dihedral pdb=" C ASP B 809 " pdb=" N ASP B 809 " pdb=" CA ASP B 809 " pdb=" CB ASP B 809 " ideal model delta harmonic sigma weight residual -122.60 -138.36 15.76 0 2.50e+00 1.60e-01 3.98e+01 dihedral pdb=" C ASP P 809 " pdb=" N ASP P 809 " pdb=" CA ASP P 809 " pdb=" CB ASP P 809 " ideal model delta harmonic sigma weight residual -122.60 -138.27 15.67 0 2.50e+00 1.60e-01 3.93e+01 ... (remaining 19588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2721 0.117 - 0.234: 694 0.234 - 0.351: 19 0.351 - 0.468: 1 0.468 - 0.584: 10 Chirality restraints: 3445 Sorted by residual: chirality pdb=" CA ASP P 809 " pdb=" N ASP P 809 " pdb=" C ASP P 809 " pdb=" CB ASP P 809 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.54e+00 chirality pdb=" CA ASP B 809 " pdb=" N ASP B 809 " pdb=" C ASP B 809 " pdb=" CB ASP B 809 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" CA ASP X 809 " pdb=" N ASP X 809 " pdb=" C ASP X 809 " pdb=" CB ASP X 809 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 3442 not shown) Planarity restraints: 6110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 808 " -0.300 9.50e-02 1.11e+02 1.12e-01 6.60e+01 pdb=" NE ARG H 808 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG H 808 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG H 808 " -0.068 2.00e-02 2.50e+03 pdb=" NH2 ARG H 808 " 0.006 2.00e-02 2.50e+03 pdb="HH11 ARG H 808 " 0.115 2.00e-02 2.50e+03 pdb="HH12 ARG H 808 " -0.040 2.00e-02 2.50e+03 pdb="HH21 ARG H 808 " 0.039 2.00e-02 2.50e+03 pdb="HH22 ARG H 808 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 795 " 0.077 2.00e-02 2.50e+03 3.84e-02 4.42e+01 pdb=" CG PHE H 795 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE H 795 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE H 795 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE H 795 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 795 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE H 795 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE H 795 " -0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE H 795 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE H 795 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE H 795 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE H 795 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 795 " 0.081 2.00e-02 2.50e+03 3.47e-02 3.61e+01 pdb=" CG PHE I 795 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE I 795 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE I 795 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE I 795 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE I 795 " -0.022 2.00e-02 2.50e+03 pdb=" CZ PHE I 795 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE I 795 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE I 795 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE I 795 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE I 795 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE I 795 " 0.065 2.00e-02 2.50e+03 ... (remaining 6107 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1634 2.19 - 2.79: 79657 2.79 - 3.39: 116471 3.39 - 4.00: 143347 4.00 - 4.60: 215566 Nonbonded interactions: 556675 Sorted by model distance: nonbonded pdb=" OD2 ASP C 834 " pdb=" HG1 THR C 837 " model vdw 1.584 2.450 nonbonded pdb=" OD2 ASP Y 834 " pdb=" HG1 THR Y 837 " model vdw 1.595 2.450 nonbonded pdb=" OD2 ASP W 834 " pdb=" HG1 THR W 837 " model vdw 1.606 2.450 nonbonded pdb=" OD2 ASP G 834 " pdb=" HG1 THR G 837 " model vdw 1.608 2.450 nonbonded pdb=" OD2 ASP S 834 " pdb=" HG1 THR S 837 " model vdw 1.617 2.450 ... (remaining 556670 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = (chain 'A1' and resid 769 through 826) selection = (chain 'A2' and resid 769 through 826) selection = (chain 'A3' and resid 769 through 826) selection = (chain 'A4' and resid 769 through 826) selection = (chain 'Ar' and resid 769 through 826) selection = (chain 'As' and resid 769 through 826) selection = (chain 'At' and resid 769 through 826) selection = (chain 'Au' and resid 769 through 826) selection = (chain 'Av' and resid 769 through 826) selection = (chain 'Aw' and resid 769 through 826) selection = (chain 'Ax' and resid 769 through 826) selection = (chain 'Ay' and resid 769 through 826) selection = (chain 'Az' and resid 769 through 826) selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } 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: 1.400 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: 0.160 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.260 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 : 0.011 0.041 20774 Z= 0.643 Angle : 1.773 7.873 27976 Z= 1.178 Chirality : 0.095 0.584 3445 Planarity : 0.013 0.101 3549 Dihedral : 15.362 89.910 8021 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.30 % Favored : 95.58 % Rotamer: Outliers : 0.62 % Allowed : 3.38 % Favored : 96.00 % Cbeta Deviations : 0.43 % 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 aren not related in a simple way. whole: -1.60 (0.14), residues: 2626 helix: -0.81 (0.09), residues: 2184 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 774 TYR 0.076 0.024 TYRAx 772 PHE 0.043 0.013 PHE C 795 Details of bonding type rmsd covalent geometry : bond 0.01055 (20774) covalent geometry : angle 1.77300 (27976) hydrogen bonds : bond 0.16365 ( 1687) hydrogen bonds : angle 6.61675 ( 4998) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 633 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8682 (mtpp) REVERT: A 798 MET cc_start: 0.8029 (mmt) cc_final: 0.7266 (mmt) REVERT: A1 791 GLU cc_start: 0.7938 (tt0) cc_final: 0.7564 (tp30) REVERT: A1 793 LYS cc_start: 0.9078 (tttt) cc_final: 0.8777 (ttpt) REVERT: A1 828 LYS cc_start: 0.7892 (tttt) cc_final: 0.7559 (ttpt) REVERT: A2 791 GLU cc_start: 0.7989 (tt0) cc_final: 0.7466 (tp30) REVERT: A3 791 GLU cc_start: 0.7974 (tt0) cc_final: 0.7431 (tp30) REVERT: A4 791 GLU cc_start: 0.8009 (tt0) cc_final: 0.7729 (tp30) REVERT: As 791 GLU cc_start: 0.7888 (tt0) cc_final: 0.7485 (tp30) REVERT: As 828 LYS cc_start: 0.8412 (tttt) cc_final: 0.8074 (tttm) REVERT: At 828 LYS cc_start: 0.8195 (tttt) cc_final: 0.7843 (ttpt) REVERT: Au 791 GLU cc_start: 0.7733 (tt0) cc_final: 0.7365 (tp30) REVERT: Aw 802 ILE cc_start: 0.9012 (mt) cc_final: 0.8787 (pt) REVERT: Aw 828 LYS cc_start: 0.8336 (tttt) cc_final: 0.7942 (ttpt) REVERT: Ax 798 MET cc_start: 0.8447 (mtt) cc_final: 0.8182 (mtt) REVERT: Az 793 LYS cc_start: 0.9030 (tttt) cc_final: 0.8811 (ttmm) REVERT: B 778 GLU cc_start: 0.8595 (tt0) cc_final: 0.8345 (tp30) REVERT: B 817 MET cc_start: 0.6396 (mmm) cc_final: 0.5807 (tpp) REVERT: C 798 MET cc_start: 0.8004 (mmt) cc_final: 0.7439 (mmt) REVERT: I 791 GLU cc_start: 0.8275 (tp30) cc_final: 0.8068 (tp30) REVERT: K 791 GLU cc_start: 0.8545 (tp30) cc_final: 0.8188 (tp30) REVERT: K 796 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8852 (mtpp) REVERT: L 778 GLU cc_start: 0.8437 (tt0) cc_final: 0.8188 (tp30) REVERT: M 776 GLN cc_start: 0.8621 (mt0) cc_final: 0.8420 (mt0) REVERT: M 791 GLU cc_start: 0.8280 (tp30) cc_final: 0.8011 (tp30) REVERT: M 796 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8565 (mtpp) REVERT: M 802 ILE cc_start: 0.8755 (pt) cc_final: 0.8386 (tt) REVERT: O 791 GLU cc_start: 0.8458 (tp30) cc_final: 0.8087 (tp30) REVERT: O 796 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8444 (mtpp) REVERT: Q 789 GLU cc_start: 0.8832 (tt0) cc_final: 0.8527 (tt0) REVERT: R 817 MET cc_start: 0.6546 (mmm) cc_final: 0.5825 (mmt) REVERT: S 798 MET cc_start: 0.7957 (mmt) cc_final: 0.7326 (mmt) REVERT: U 789 GLU cc_start: 0.8816 (tt0) cc_final: 0.8528 (tm-30) REVERT: U 790 VAL cc_start: 0.8854 (t) cc_final: 0.8583 (t) REVERT: U 830 THR cc_start: 0.8818 (m) cc_final: 0.8527 (t) REVERT: W 798 MET cc_start: 0.8073 (mmt) cc_final: 0.7153 (mmm) REVERT: W 817 MET cc_start: 0.7990 (tpt) cc_final: 0.7717 (tpp) REVERT: Y 791 GLU cc_start: 0.8381 (tp30) cc_final: 0.8139 (tp30) REVERT: Z 778 GLU cc_start: 0.8528 (tt0) cc_final: 0.8135 (tp30) outliers start: 14 outliers final: 3 residues processed: 645 average time/residue: 0.3784 time to fit residues: 339.8070 Evaluate side-chains 328 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 325 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain Y residue 837 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 797 GLN C 776 GLN F 797 GLN H 797 GLN I 797 GLN ** J 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 797 GLN M 776 GLN M 797 GLN O 776 GLN O 797 GLN P 797 GLN Q 776 GLN ** R 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 776 GLN U 776 GLN U 797 GLN V 797 GLN W 776 GLN W 797 GLN Y 797 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.074334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.064778 restraints weight = 218304.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066464 restraints weight = 90268.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067488 restraints weight = 51974.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.068079 restraints weight = 37633.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.068387 restraints weight = 31410.810| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20774 Z= 0.261 Angle : 0.693 5.172 27976 Z= 0.374 Chirality : 0.040 0.164 3445 Planarity : 0.005 0.045 3549 Dihedral : 5.500 53.976 2787 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.27 % Allowed : 9.83 % Favored : 87.91 % 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 aren not related in a simple way. whole: 0.65 (0.15), residues: 2626 helix: 0.89 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 774 TYR 0.018 0.002 TYRAt 772 PHE 0.015 0.002 PHE K 846 Details of bonding type rmsd covalent geometry : bond 0.00566 (20774) covalent geometry : angle 0.69306 (27976) hydrogen bonds : bond 0.04598 ( 1687) hydrogen bonds : angle 4.49005 ( 4998) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8657 (mtmt) cc_final: 0.8309 (mtpp) REVERT: As 808 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6969 (ptm160) REVERT: Aw 802 ILE cc_start: 0.8875 (mt) cc_final: 0.8557 (pt) REVERT: Ax 780 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7662 (tm-30) REVERT: Ax 798 MET cc_start: 0.8351 (mtt) cc_final: 0.8064 (mtt) REVERT: Ay 780 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7830 (tm-30) REVERT: E 798 MET cc_start: 0.7982 (mmt) cc_final: 0.7712 (mmt) REVERT: F 791 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7378 (tm-30) REVERT: G 821 LEU cc_start: 0.8662 (mt) cc_final: 0.8257 (mt) REVERT: I 791 GLU cc_start: 0.8096 (tp30) cc_final: 0.7892 (tp30) REVERT: K 791 GLU cc_start: 0.8197 (tp30) cc_final: 0.7914 (tp30) REVERT: K 802 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8456 (tt) REVERT: M 791 GLU cc_start: 0.8097 (tp30) cc_final: 0.7856 (tp30) REVERT: M 802 ILE cc_start: 0.8398 (pt) cc_final: 0.8161 (tt) REVERT: O 791 GLU cc_start: 0.8112 (tp30) cc_final: 0.7803 (tp30) REVERT: O 796 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8396 (mtpp) REVERT: Q 789 GLU cc_start: 0.8675 (tt0) cc_final: 0.8439 (tt0) REVERT: R 822 LEU cc_start: 0.8075 (mt) cc_final: 0.7674 (tt) REVERT: S 789 GLU cc_start: 0.8595 (tt0) cc_final: 0.8331 (tm-30) REVERT: U 789 GLU cc_start: 0.8649 (tt0) cc_final: 0.8313 (tt0) REVERT: V 796 LYS cc_start: 0.8883 (tmtt) cc_final: 0.8657 (tptp) REVERT: W 791 GLU cc_start: 0.8354 (tp30) cc_final: 0.8092 (tp30) REVERT: Y 791 GLU cc_start: 0.8336 (tp30) cc_final: 0.8123 (tp30) REVERT: Z 817 MET cc_start: 0.6836 (mmm) cc_final: 0.6468 (tpp) outliers start: 51 outliers final: 39 residues processed: 361 average time/residue: 0.2506 time to fit residues: 144.2392 Evaluate side-chains 301 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 800 GLU Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain As residue 824 SER Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Av residue 800 GLU Chi-restraints excluded: chain Aw residue 807 ILE Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 821 LEU Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 819 VAL Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain G residue 807 ILE Chi-restraints excluded: chain G residue 819 VAL Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain K residue 802 ILE Chi-restraints excluded: chain K residue 819 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain L residue 822 LEU Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain Q residue 819 VAL Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain S residue 819 VAL Chi-restraints excluded: chain S residue 839 ILE Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain V residue 822 LEU Chi-restraints excluded: chain W residue 790 VAL Chi-restraints excluded: chain Y residue 837 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 77 optimal weight: 8.9990 chunk 222 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN A1 776 GLN Ay 776 GLN M 776 GLN R 797 GLN W 776 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.074594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.065221 restraints weight = 218168.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066889 restraints weight = 89805.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067892 restraints weight = 51569.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.068461 restraints weight = 37413.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068776 restraints weight = 31360.319| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20774 Z= 0.184 Angle : 0.574 4.521 27976 Z= 0.304 Chirality : 0.036 0.148 3445 Planarity : 0.004 0.042 3549 Dihedral : 4.891 55.444 2787 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.00 % Allowed : 11.47 % Favored : 86.53 % 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 aren not related in a simple way. whole: 1.49 (0.16), residues: 2626 helix: 1.48 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 808 TYR 0.011 0.001 TYRA1 772 PHE 0.007 0.001 PHE I 795 Details of bonding type rmsd covalent geometry : bond 0.00383 (20774) covalent geometry : angle 0.57410 (27976) hydrogen bonds : bond 0.03851 ( 1687) hydrogen bonds : angle 3.98099 ( 4998) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8298 (mtpp) REVERT: A1 793 LYS cc_start: 0.9183 (tttm) cc_final: 0.8917 (ttmm) REVERT: A3 780 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7688 (tm-30) REVERT: A4 802 ILE cc_start: 0.8967 (mt) cc_final: 0.8700 (tp) REVERT: As 808 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6912 (ptm160) REVERT: At 780 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7724 (tm-30) REVERT: Au 780 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7742 (tm-30) REVERT: Ax 780 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7708 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7901 (tm-30) REVERT: E 789 GLU cc_start: 0.8360 (tt0) cc_final: 0.8142 (tt0) REVERT: G 791 GLU cc_start: 0.8175 (tp30) cc_final: 0.7818 (tp30) REVERT: I 791 GLU cc_start: 0.8076 (tp30) cc_final: 0.7860 (tp30) REVERT: K 791 GLU cc_start: 0.8207 (tp30) cc_final: 0.7928 (tp30) REVERT: K 792 VAL cc_start: 0.9300 (t) cc_final: 0.9033 (p) REVERT: K 796 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8834 (mtpp) REVERT: L 797 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: M 791 GLU cc_start: 0.8108 (tp30) cc_final: 0.7862 (tp30) REVERT: M 792 VAL cc_start: 0.9248 (t) cc_final: 0.9037 (p) REVERT: M 802 ILE cc_start: 0.8384 (pt) cc_final: 0.8169 (tt) REVERT: O 791 GLU cc_start: 0.8142 (tp30) cc_final: 0.7802 (tp30) REVERT: O 796 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8378 (mtpp) REVERT: P 791 GLU cc_start: 0.8015 (tp30) cc_final: 0.7541 (tp30) REVERT: Q 789 GLU cc_start: 0.8588 (tt0) cc_final: 0.8353 (tt0) REVERT: R 791 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7560 (tm-30) REVERT: S 789 GLU cc_start: 0.8576 (tt0) cc_final: 0.8317 (tm-30) REVERT: S 792 VAL cc_start: 0.9264 (t) cc_final: 0.9060 (p) REVERT: V 796 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8690 (tptp) REVERT: W 791 GLU cc_start: 0.8332 (tp30) cc_final: 0.8025 (tp30) REVERT: Y 791 GLU cc_start: 0.8266 (tp30) cc_final: 0.8031 (tp30) outliers start: 45 outliers final: 37 residues processed: 346 average time/residue: 0.2448 time to fit residues: 137.1019 Evaluate side-chains 313 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 793 LYS Chi-restraints excluded: chain A2 residue 800 GLU Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain Ar residue 824 SER Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Av residue 800 GLU Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 821 LEU Chi-restraints excluded: chain Ay residue 791 GLU Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain G residue 807 ILE Chi-restraints excluded: chain G residue 819 VAL Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain J residue 792 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain L residue 797 GLN Chi-restraints excluded: chain L residue 822 LEU Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain M residue 807 ILE Chi-restraints excluded: chain O residue 819 VAL Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain V residue 822 LEU Chi-restraints excluded: chain Y residue 807 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 188 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN A1 776 GLN Ax 776 GLN G 776 GLN M 776 GLN Q 785 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.074405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064960 restraints weight = 218084.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066631 restraints weight = 90688.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.067626 restraints weight = 52290.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068198 restraints weight = 37896.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068498 restraints weight = 31781.841| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20774 Z= 0.191 Angle : 0.555 4.446 27976 Z= 0.294 Chirality : 0.036 0.149 3445 Planarity : 0.004 0.043 3549 Dihedral : 4.634 56.366 2786 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.09 % Allowed : 12.32 % Favored : 85.59 % 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 aren not related in a simple way. whole: 1.98 (0.16), residues: 2626 helix: 1.82 (0.11), residues: 2158 sheet: None (None), residues: 0 loop : -1.07 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAv 808 TYR 0.012 0.001 TYRA1 772 PHE 0.010 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00405 (20774) covalent geometry : angle 0.55550 (27976) hydrogen bonds : bond 0.03609 ( 1687) hydrogen bonds : angle 3.85201 ( 4998) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8467 (mtpp) REVERT: A 802 ILE cc_start: 0.8844 (pt) cc_final: 0.8637 (tt) REVERT: A2 817 MET cc_start: 0.7222 (OUTLIER) cc_final: 0.6889 (mpt) REVERT: A3 780 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A4 802 ILE cc_start: 0.8978 (mt) cc_final: 0.8671 (tp) REVERT: As 780 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7930 (tm-30) REVERT: As 808 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6834 (ptm160) REVERT: Au 780 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7693 (tm-30) REVERT: Au 796 LYS cc_start: 0.8844 (tttt) cc_final: 0.8610 (tptt) REVERT: Ax 780 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7796 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 789 GLU cc_start: 0.8382 (tt0) cc_final: 0.8144 (tt0) REVERT: F 791 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7586 (tm-30) REVERT: G 791 GLU cc_start: 0.8213 (tp30) cc_final: 0.7846 (tp30) REVERT: K 791 GLU cc_start: 0.8257 (tp30) cc_final: 0.7958 (tp30) REVERT: K 792 VAL cc_start: 0.9293 (t) cc_final: 0.9033 (p) REVERT: K 796 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8843 (mtpp) REVERT: L 797 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: M 791 GLU cc_start: 0.8154 (tp30) cc_final: 0.7849 (tp30) REVERT: M 792 VAL cc_start: 0.9249 (t) cc_final: 0.8959 (p) REVERT: M 802 ILE cc_start: 0.8371 (pt) cc_final: 0.8152 (tt) REVERT: O 791 GLU cc_start: 0.8169 (tp30) cc_final: 0.7847 (tp30) REVERT: O 796 LYS cc_start: 0.8822 (mtmt) cc_final: 0.8364 (mtpp) REVERT: P 791 GLU cc_start: 0.7926 (tp30) cc_final: 0.7445 (tp30) REVERT: Q 789 GLU cc_start: 0.8542 (tt0) cc_final: 0.8230 (tt0) REVERT: R 791 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7666 (tm-30) REVERT: S 789 GLU cc_start: 0.8594 (tt0) cc_final: 0.8321 (tm-30) REVERT: W 791 GLU cc_start: 0.8174 (tp30) cc_final: 0.7819 (tp30) REVERT: Y 791 GLU cc_start: 0.8334 (tp30) cc_final: 0.8062 (tp30) outliers start: 47 outliers final: 37 residues processed: 331 average time/residue: 0.2353 time to fit residues: 127.5315 Evaluate side-chains 313 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 793 LYS Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 817 MET Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain Ar residue 824 SER Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 800 GLU Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Av residue 800 GLU Chi-restraints excluded: chain Av residue 822 LEU Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 821 LEU Chi-restraints excluded: chain Ax residue 830 THR Chi-restraints excluded: chain Ay residue 791 GLU Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Ay residue 824 SER Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain G residue 780 GLU Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain L residue 797 GLN Chi-restraints excluded: chain L residue 822 LEU Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain M residue 807 ILE Chi-restraints excluded: chain Q residue 806 THR Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain S residue 807 ILE Chi-restraints excluded: chain V residue 792 VAL Chi-restraints excluded: chain V residue 822 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 42 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 219 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN M 776 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.075744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.066304 restraints weight = 215946.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067991 restraints weight = 89262.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068992 restraints weight = 51086.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.069559 restraints weight = 37237.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069821 restraints weight = 31186.945| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20774 Z= 0.104 Angle : 0.483 5.191 27976 Z= 0.250 Chirality : 0.034 0.149 3445 Planarity : 0.003 0.034 3549 Dihedral : 4.204 55.080 2786 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 13.61 % Favored : 84.75 % 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 aren not related in a simple way. whole: 2.82 (0.16), residues: 2626 helix: 2.34 (0.11), residues: 2184 sheet: None (None), residues: 0 loop : -0.59 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 808 TYR 0.013 0.001 TYRAx 772 PHE 0.006 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00225 (20774) covalent geometry : angle 0.48329 (27976) hydrogen bonds : bond 0.03069 ( 1687) hydrogen bonds : angle 3.38361 ( 4998) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 335 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8425 (mtpp) REVERT: A1 793 LYS cc_start: 0.9202 (tttm) cc_final: 0.8958 (ttmm) REVERT: A2 817 MET cc_start: 0.7234 (OUTLIER) cc_final: 0.6892 (mpt) REVERT: A3 780 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A4 802 ILE cc_start: 0.8971 (mt) cc_final: 0.8722 (tp) REVERT: As 780 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7814 (tm-30) REVERT: As 808 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6769 (ptm160) REVERT: Au 796 LYS cc_start: 0.8831 (tttt) cc_final: 0.8612 (tptt) REVERT: Ax 780 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7733 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 791 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7779 (tm-30) REVERT: D 791 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7287 (tm-30) REVERT: E 789 GLU cc_start: 0.8375 (tt0) cc_final: 0.8137 (tt0) REVERT: F 822 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7463 (tp) REVERT: I 791 GLU cc_start: 0.7940 (tp30) cc_final: 0.7673 (tp30) REVERT: K 791 GLU cc_start: 0.8208 (tp30) cc_final: 0.7947 (tp30) REVERT: K 792 VAL cc_start: 0.9316 (t) cc_final: 0.9081 (p) REVERT: K 796 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8800 (mtpp) REVERT: M 791 GLU cc_start: 0.8153 (tp30) cc_final: 0.7786 (tp30) REVERT: M 792 VAL cc_start: 0.9255 (t) cc_final: 0.8945 (p) REVERT: M 802 ILE cc_start: 0.8231 (pt) cc_final: 0.8015 (tt) REVERT: O 791 GLU cc_start: 0.8218 (tp30) cc_final: 0.7861 (tp30) REVERT: O 796 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8437 (mtpp) REVERT: P 791 GLU cc_start: 0.7935 (tp30) cc_final: 0.7708 (tp30) REVERT: Q 789 GLU cc_start: 0.8544 (tt0) cc_final: 0.8320 (tt0) REVERT: Q 798 MET cc_start: 0.7871 (mmt) cc_final: 0.7568 (mmt) REVERT: R 791 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7662 (tm-30) REVERT: T 817 MET cc_start: 0.7195 (mmm) cc_final: 0.6678 (tpp) REVERT: W 791 GLU cc_start: 0.8313 (tp30) cc_final: 0.7852 (tp30) REVERT: Y 791 GLU cc_start: 0.8252 (tp30) cc_final: 0.8015 (tp30) outliers start: 37 outliers final: 24 residues processed: 361 average time/residue: 0.2397 time to fit residues: 140.5162 Evaluate side-chains 316 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 289 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 822 LEU Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 800 GLU Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 830 THR Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain G residue 807 ILE Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain M residue 807 ILE Chi-restraints excluded: chain Q residue 806 THR Chi-restraints excluded: chain Q residue 822 LEU Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain V residue 822 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 57 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN E 776 GLN F 797 GLN L 797 GLN M 776 GLN U 785 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065382 restraints weight = 217947.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067052 restraints weight = 90227.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068067 restraints weight = 51736.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068640 restraints weight = 37493.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068958 restraints weight = 31383.052| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20774 Z= 0.150 Angle : 0.515 6.803 27976 Z= 0.270 Chirality : 0.035 0.149 3445 Planarity : 0.004 0.036 3549 Dihedral : 4.161 53.851 2785 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.65 % Allowed : 14.58 % Favored : 83.77 % 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 aren not related in a simple way. whole: 2.82 (0.16), residues: 2626 helix: 2.36 (0.11), residues: 2197 sheet: None (None), residues: 0 loop : -0.86 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGAv 808 TYR 0.011 0.001 TYRAx 772 PHE 0.007 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00319 (20774) covalent geometry : angle 0.51460 (27976) hydrogen bonds : bond 0.03176 ( 1687) hydrogen bonds : angle 3.46302 ( 4998) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 289 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8434 (mtpp) REVERT: A2 817 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7019 (mpt) REVERT: A3 780 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A4 802 ILE cc_start: 0.8959 (mt) cc_final: 0.8704 (tp) REVERT: As 780 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7885 (tm-30) REVERT: As 808 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6800 (ptm160) REVERT: Au 796 LYS cc_start: 0.8737 (tttt) cc_final: 0.8495 (tptt) REVERT: Ax 780 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7796 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7979 (tm-30) REVERT: B 817 MET cc_start: 0.7030 (tpp) cc_final: 0.6821 (tpt) REVERT: D 791 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7338 (tm-30) REVERT: E 789 GLU cc_start: 0.8413 (tt0) cc_final: 0.8181 (tt0) REVERT: F 822 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7446 (tp) REVERT: I 791 GLU cc_start: 0.8104 (tp30) cc_final: 0.7766 (tp30) REVERT: K 791 GLU cc_start: 0.8291 (tp30) cc_final: 0.7935 (tp30) REVERT: K 796 LYS cc_start: 0.9107 (mtmt) cc_final: 0.8681 (mtpp) REVERT: L 791 GLU cc_start: 0.7945 (tp30) cc_final: 0.7725 (tm-30) REVERT: M 789 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7632 (tm-30) REVERT: M 791 GLU cc_start: 0.8153 (tp30) cc_final: 0.7790 (tp30) REVERT: M 792 VAL cc_start: 0.9242 (t) cc_final: 0.8941 (p) REVERT: M 802 ILE cc_start: 0.8282 (pt) cc_final: 0.8026 (tt) REVERT: O 791 GLU cc_start: 0.8231 (tp30) cc_final: 0.7859 (tp30) REVERT: O 796 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8400 (mtpp) REVERT: P 791 GLU cc_start: 0.7961 (tp30) cc_final: 0.7487 (tp30) REVERT: Q 798 MET cc_start: 0.7895 (mmt) cc_final: 0.7565 (mmt) REVERT: R 791 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7639 (tm-30) REVERT: T 817 MET cc_start: 0.7107 (mmm) cc_final: 0.6564 (tpp) REVERT: U 789 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7828 (tm-30) REVERT: W 791 GLU cc_start: 0.8289 (tp30) cc_final: 0.7884 (tp30) REVERT: Y 791 GLU cc_start: 0.8353 (tp30) cc_final: 0.8080 (tp30) outliers start: 37 outliers final: 29 residues processed: 317 average time/residue: 0.2557 time to fit residues: 132.4070 Evaluate side-chains 307 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 793 LYS Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 822 LEU Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain Ar residue 824 SER Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 800 GLU Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Aw residue 800 GLU Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 830 THR Chi-restraints excluded: chain Ay residue 798 MET Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Ay residue 824 SER Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain O residue 822 LEU Chi-restraints excluded: chain Q residue 822 LEU Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain V residue 822 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 94 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN D 797 GLN M 776 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.074841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.065459 restraints weight = 217797.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.067119 restraints weight = 90315.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.068112 restraints weight = 51990.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068672 restraints weight = 37906.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068986 restraints weight = 31880.075| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20774 Z= 0.163 Angle : 0.521 8.067 27976 Z= 0.273 Chirality : 0.035 0.148 3445 Planarity : 0.004 0.036 3549 Dihedral : 4.168 53.656 2785 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.87 % Allowed : 14.32 % Favored : 83.82 % 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 aren not related in a simple way. whole: 2.84 (0.16), residues: 2626 helix: 2.46 (0.11), residues: 2171 sheet: None (None), residues: 0 loop : -1.17 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 808 TYR 0.009 0.001 TYRAx 772 PHE 0.007 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00346 (20774) covalent geometry : angle 0.52107 (27976) hydrogen bonds : bond 0.03234 ( 1687) hydrogen bonds : angle 3.47691 ( 4998) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8892 (mtmt) cc_final: 0.8496 (mtpp) REVERT: A2 817 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6915 (mpt) REVERT: A3 780 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7811 (tm-30) REVERT: As 780 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7920 (tm-30) REVERT: As 808 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6872 (ptm160) REVERT: At 780 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7832 (tm-30) REVERT: Au 796 LYS cc_start: 0.8744 (tttt) cc_final: 0.8491 (tptt) REVERT: Ax 780 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7857 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 791 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7783 (tm-30) REVERT: B 817 MET cc_start: 0.7142 (tpp) cc_final: 0.6930 (tpt) REVERT: D 791 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7370 (tm-30) REVERT: E 789 GLU cc_start: 0.8469 (tt0) cc_final: 0.8214 (tt0) REVERT: F 822 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7380 (tp) REVERT: G 791 GLU cc_start: 0.8318 (tp30) cc_final: 0.7939 (tp30) REVERT: I 791 GLU cc_start: 0.8132 (tp30) cc_final: 0.7738 (tp30) REVERT: K 791 GLU cc_start: 0.8305 (tp30) cc_final: 0.7949 (tp30) REVERT: K 796 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8701 (mtpp) REVERT: L 791 GLU cc_start: 0.7932 (tp30) cc_final: 0.7721 (tm-30) REVERT: M 789 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7721 (tm-30) REVERT: M 791 GLU cc_start: 0.8165 (tp30) cc_final: 0.7850 (tp30) REVERT: M 792 VAL cc_start: 0.9254 (t) cc_final: 0.8935 (p) REVERT: M 802 ILE cc_start: 0.8185 (pt) cc_final: 0.7941 (tt) REVERT: N 791 GLU cc_start: 0.8005 (tp30) cc_final: 0.7775 (tm-30) REVERT: O 791 GLU cc_start: 0.8229 (tp30) cc_final: 0.7851 (tp30) REVERT: O 796 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8395 (mtpp) REVERT: P 791 GLU cc_start: 0.7985 (tp30) cc_final: 0.7503 (tp30) REVERT: R 791 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7736 (tm-30) REVERT: T 817 MET cc_start: 0.7157 (mmm) cc_final: 0.6663 (tpp) REVERT: U 789 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7805 (tm-30) REVERT: W 791 GLU cc_start: 0.8308 (tp30) cc_final: 0.7899 (tp30) REVERT: Y 791 GLU cc_start: 0.8363 (tp30) cc_final: 0.8057 (tp30) outliers start: 42 outliers final: 33 residues processed: 317 average time/residue: 0.2565 time to fit residues: 131.5866 Evaluate side-chains 305 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 780 GLU Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 793 LYS Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 822 LEU Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain Ar residue 824 SER Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 802 ILE Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 800 GLU Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 830 THR Chi-restraints excluded: chain Ay residue 798 MET Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Ay residue 824 SER Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain G residue 822 LEU Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain O residue 822 LEU Chi-restraints excluded: chain Q residue 806 THR Chi-restraints excluded: chain Q residue 822 LEU Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain V residue 822 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 158 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.075034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.065563 restraints weight = 218272.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067234 restraints weight = 89956.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.068236 restraints weight = 51514.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.068795 restraints weight = 37560.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069093 restraints weight = 31553.636| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20774 Z= 0.134 Angle : 0.504 8.182 27976 Z= 0.262 Chirality : 0.034 0.149 3445 Planarity : 0.004 0.034 3549 Dihedral : 4.049 53.306 2785 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 14.36 % Favored : 83.90 % 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 aren not related in a simple way. whole: 3.13 (0.16), residues: 2626 helix: 2.58 (0.11), residues: 2197 sheet: None (None), residues: 0 loop : -0.78 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 808 TYR 0.008 0.001 TYRAx 772 PHE 0.007 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00290 (20774) covalent geometry : angle 0.50401 (27976) hydrogen bonds : bond 0.03071 ( 1687) hydrogen bonds : angle 3.35702 ( 4998) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 301 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8517 (mtpp) REVERT: A1 802 ILE cc_start: 0.8935 (mt) cc_final: 0.8597 (tp) REVERT: A2 817 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6887 (mpt) REVERT: A3 780 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7776 (tm-30) REVERT: As 780 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7884 (tm-30) REVERT: As 808 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6815 (ptm160) REVERT: Ax 780 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7854 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7998 (tm-30) REVERT: D 791 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7437 (tm-30) REVERT: E 789 GLU cc_start: 0.8422 (tt0) cc_final: 0.8203 (tt0) REVERT: F 822 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7305 (tp) REVERT: G 791 GLU cc_start: 0.8290 (tp30) cc_final: 0.7894 (tp30) REVERT: I 791 GLU cc_start: 0.8156 (tp30) cc_final: 0.7757 (tp30) REVERT: K 791 GLU cc_start: 0.8232 (tp30) cc_final: 0.7829 (tp30) REVERT: K 796 LYS cc_start: 0.8996 (mtmt) cc_final: 0.8782 (mtpp) REVERT: M 789 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7686 (tm-30) REVERT: M 791 GLU cc_start: 0.8146 (tp30) cc_final: 0.7833 (tp30) REVERT: M 792 VAL cc_start: 0.9255 (t) cc_final: 0.8949 (p) REVERT: M 802 ILE cc_start: 0.8121 (pt) cc_final: 0.7890 (tt) REVERT: O 789 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7829 (tm-30) REVERT: O 791 GLU cc_start: 0.8219 (tp30) cc_final: 0.7865 (tp30) REVERT: O 796 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8332 (mtpp) REVERT: P 791 GLU cc_start: 0.8027 (tp30) cc_final: 0.7576 (tp30) REVERT: P 794 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9033 (ttmm) REVERT: R 791 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7683 (tm-30) REVERT: T 817 MET cc_start: 0.7095 (mmm) cc_final: 0.6641 (tpp) REVERT: U 789 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7814 (tm-30) REVERT: W 791 GLU cc_start: 0.8292 (tp30) cc_final: 0.7872 (tp30) REVERT: Y 791 GLU cc_start: 0.8338 (tp30) cc_final: 0.8041 (tp30) outliers start: 39 outliers final: 31 residues processed: 331 average time/residue: 0.2490 time to fit residues: 133.3590 Evaluate side-chains 315 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 822 LEU Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain Ar residue 824 SER Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 800 GLU Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 830 THR Chi-restraints excluded: chain Ay residue 798 MET Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Ay residue 824 SER Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain Az residue 824 SER Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain F residue 822 LEU Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain O residue 822 LEU Chi-restraints excluded: chain Q residue 806 THR Chi-restraints excluded: chain Q residue 822 LEU Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain V residue 822 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 150 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 163 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN J 797 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.065796 restraints weight = 217624.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067440 restraints weight = 89672.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068435 restraints weight = 51580.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.068985 restraints weight = 37711.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069271 restraints weight = 31651.344| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20774 Z= 0.138 Angle : 0.510 7.756 27976 Z= 0.265 Chirality : 0.034 0.149 3445 Planarity : 0.004 0.035 3549 Dihedral : 4.015 52.807 2785 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.82 % Allowed : 14.50 % Favored : 83.68 % 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 aren not related in a simple way. whole: 3.24 (0.16), residues: 2626 helix: 2.66 (0.11), residues: 2197 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 808 TYR 0.007 0.001 TYRAx 772 PHE 0.007 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00299 (20774) covalent geometry : angle 0.51003 (27976) hydrogen bonds : bond 0.03057 ( 1687) hydrogen bonds : angle 3.34434 ( 4998) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8896 (mtmt) cc_final: 0.8522 (mtpp) REVERT: A1 802 ILE cc_start: 0.8889 (mt) cc_final: 0.8575 (tp) REVERT: A2 817 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6865 (mpt) REVERT: A3 780 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7778 (tm-30) REVERT: As 780 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7885 (tm-30) REVERT: As 796 LYS cc_start: 0.8816 (tttt) cc_final: 0.8588 (tptt) REVERT: As 808 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6827 (ptm160) REVERT: Ax 780 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7835 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7991 (tm-30) REVERT: D 791 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7441 (tm-30) REVERT: E 789 GLU cc_start: 0.8414 (tt0) cc_final: 0.8197 (tt0) REVERT: G 791 GLU cc_start: 0.8282 (tp30) cc_final: 0.7892 (tp30) REVERT: I 791 GLU cc_start: 0.8156 (tp30) cc_final: 0.7758 (tp30) REVERT: K 791 GLU cc_start: 0.8224 (tp30) cc_final: 0.7874 (tp30) REVERT: L 791 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7585 (tm-30) REVERT: M 789 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7695 (tm-30) REVERT: M 791 GLU cc_start: 0.8154 (tp30) cc_final: 0.7832 (tp30) REVERT: M 792 VAL cc_start: 0.9257 (t) cc_final: 0.8950 (p) REVERT: M 802 ILE cc_start: 0.8118 (pt) cc_final: 0.7882 (tt) REVERT: N 791 GLU cc_start: 0.7999 (tp30) cc_final: 0.7771 (tm-30) REVERT: O 789 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7811 (tm-30) REVERT: O 791 GLU cc_start: 0.8199 (tp30) cc_final: 0.7841 (tp30) REVERT: O 796 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8330 (mtpp) REVERT: P 791 GLU cc_start: 0.8025 (tp30) cc_final: 0.7581 (tp30) REVERT: P 794 LYS cc_start: 0.9376 (ttmm) cc_final: 0.9043 (ttmm) REVERT: R 791 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7678 (tm-30) REVERT: T 817 MET cc_start: 0.7107 (mmm) cc_final: 0.6648 (tpp) REVERT: U 789 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7819 (tm-30) REVERT: W 791 GLU cc_start: 0.8294 (tp30) cc_final: 0.7875 (tp30) REVERT: Y 791 GLU cc_start: 0.8326 (tp30) cc_final: 0.8031 (tp30) outliers start: 41 outliers final: 35 residues processed: 319 average time/residue: 0.2452 time to fit residues: 127.4130 Evaluate side-chains 320 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 780 GLU Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A3 residue 800 GLU Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 822 LEU Chi-restraints excluded: chain A4 residue 824 SER Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain Ar residue 824 SER Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 802 ILE Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 800 GLU Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Aw residue 800 GLU Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ax residue 830 THR Chi-restraints excluded: chain Ay residue 798 MET Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Ay residue 824 SER Chi-restraints excluded: chain Az residue 800 GLU Chi-restraints excluded: chain Az residue 824 SER Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain D residue 809 ASP Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain G residue 822 LEU Chi-restraints excluded: chain I residue 819 VAL Chi-restraints excluded: chain K residue 834 ASP Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain O residue 822 LEU Chi-restraints excluded: chain Q residue 806 THR Chi-restraints excluded: chain Q residue 822 LEU Chi-restraints excluded: chain R residue 792 VAL Chi-restraints excluded: chain V residue 822 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 37 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.075984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.066653 restraints weight = 215972.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.068306 restraints weight = 88641.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.069318 restraints weight = 50876.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069878 restraints weight = 36976.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.070196 restraints weight = 30998.159| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20774 Z= 0.101 Angle : 0.493 7.830 27976 Z= 0.252 Chirality : 0.033 0.150 3445 Planarity : 0.003 0.032 3549 Dihedral : 3.810 51.080 2785 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.20 % Allowed : 15.38 % Favored : 83.41 % 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 aren not related in a simple way. whole: 3.65 (0.16), residues: 2626 helix: 2.96 (0.11), residues: 2197 sheet: None (None), residues: 0 loop : -0.71 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 808 TYR 0.007 0.001 TYRAx 772 PHE 0.008 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00230 (20774) covalent geometry : angle 0.49275 (27976) hydrogen bonds : bond 0.02777 ( 1687) hydrogen bonds : angle 3.13440 ( 4998) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5252 Ramachandran restraints generated. 2626 Oldfield, 0 Emsley, 2626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 323 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8514 (mtpp) REVERT: A1 802 ILE cc_start: 0.8864 (mt) cc_final: 0.8557 (tp) REVERT: A2 817 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7005 (mpt) REVERT: A3 780 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7790 (tm-30) REVERT: As 780 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7848 (tm-30) REVERT: As 796 LYS cc_start: 0.8827 (tttt) cc_final: 0.8604 (tptt) REVERT: As 808 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6648 (ptm160) REVERT: At 780 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7819 (tm-30) REVERT: Ax 780 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7744 (tm-30) REVERT: Ay 780 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 791 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7462 (tm-30) REVERT: G 789 GLU cc_start: 0.8192 (tt0) cc_final: 0.7964 (tt0) REVERT: G 791 GLU cc_start: 0.8314 (tp30) cc_final: 0.7906 (tp30) REVERT: I 791 GLU cc_start: 0.8037 (tp30) cc_final: 0.7625 (tp30) REVERT: K 791 GLU cc_start: 0.8116 (tp30) cc_final: 0.7835 (tp30) REVERT: L 791 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7467 (tm-30) REVERT: M 789 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7636 (tm-30) REVERT: M 791 GLU cc_start: 0.8143 (tp30) cc_final: 0.7809 (tp30) REVERT: M 802 ILE cc_start: 0.8023 (pt) cc_final: 0.7819 (tt) REVERT: O 789 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7807 (tm-30) REVERT: O 791 GLU cc_start: 0.8200 (tp30) cc_final: 0.7852 (tp30) REVERT: O 796 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8406 (mtpp) REVERT: P 794 LYS cc_start: 0.9364 (ttmm) cc_final: 0.9043 (ttmm) REVERT: Q 789 GLU cc_start: 0.8444 (tt0) cc_final: 0.8238 (tt0) REVERT: Q 798 MET cc_start: 0.7913 (mmt) cc_final: 0.7589 (mmt) REVERT: R 791 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7664 (tm-30) REVERT: T 817 MET cc_start: 0.7054 (mmm) cc_final: 0.6748 (tpp) REVERT: U 789 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7851 (tm-30) REVERT: W 791 GLU cc_start: 0.8283 (tp30) cc_final: 0.7820 (tp30) REVERT: Y 791 GLU cc_start: 0.8329 (tp30) cc_final: 0.8124 (tp30) REVERT: Y 817 MET cc_start: 0.7189 (tmm) cc_final: 0.6896 (ppp) outliers start: 27 outliers final: 20 residues processed: 340 average time/residue: 0.2413 time to fit residues: 134.5253 Evaluate side-chains 318 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 780 GLU Chi-restraints excluded: chain A1 residue 800 GLU Chi-restraints excluded: chain A2 residue 817 MET Chi-restraints excluded: chain A2 residue 824 SER Chi-restraints excluded: chain A4 residue 800 GLU Chi-restraints excluded: chain A4 residue 822 LEU Chi-restraints excluded: chain Ar residue 800 GLU Chi-restraints excluded: chain As residue 800 GLU Chi-restraints excluded: chain As residue 802 ILE Chi-restraints excluded: chain As residue 808 ARG Chi-restraints excluded: chain Au residue 824 SER Chi-restraints excluded: chain Ax residue 800 GLU Chi-restraints excluded: chain Ay residue 800 GLU Chi-restraints excluded: chain Az residue 824 SER Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 807 ILE Chi-restraints excluded: chain M residue 806 THR Chi-restraints excluded: chain O residue 822 LEU Chi-restraints excluded: chain Q residue 806 THR Chi-restraints excluded: chain Q residue 822 LEU Chi-restraints excluded: chain R residue 792 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 8 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.075808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066535 restraints weight = 219818.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068201 restraints weight = 90359.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.069190 restraints weight = 51608.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069750 restraints weight = 37641.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070006 restraints weight = 31492.624| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20774 Z= 0.108 Angle : 0.496 7.419 27976 Z= 0.255 Chirality : 0.034 0.149 3445 Planarity : 0.003 0.034 3549 Dihedral : 3.792 50.323 2785 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.16 % Allowed : 15.87 % Favored : 82.97 % 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 aren not related in a simple way. whole: 3.73 (0.16), residues: 2626 helix: 3.02 (0.10), residues: 2197 sheet: None (None), residues: 0 loop : -0.74 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 808 TYR 0.007 0.001 TYRAx 772 PHE 0.006 0.001 PHEA3 795 Details of bonding type rmsd covalent geometry : bond 0.00243 (20774) covalent geometry : angle 0.49630 (27976) hydrogen bonds : bond 0.02797 ( 1687) hydrogen bonds : angle 3.14945 ( 4998) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4846.00 seconds wall clock time: 83 minutes 25.26 seconds (5005.26 seconds total)