Starting phenix.real_space_refine on Thu Sep 18 19:28:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivr_60933/09_2025/9ivr_60933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivr_60933/09_2025/9ivr_60933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivr_60933/09_2025/9ivr_60933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivr_60933/09_2025/9ivr_60933.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivr_60933/09_2025/9ivr_60933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivr_60933/09_2025/9ivr_60933.cif" } resolution = 2.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 12487 2.51 5 N 3497 2.21 5 O 3685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "L" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "I" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "P" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "N" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "M" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "O" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "V" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "U" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "R" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "Q" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "S" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "X" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "W" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} bond proxies already assigned to first conformer: 1101 Chain: "G" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "H" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "F" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "J" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS E 73 " occ=0.44 ... (10 atoms not shown) pdb=" SG BCYS E 73 " occ=0.56 Time building chain proxies: 5.01, per 1000 atoms: 0.25 Number of scatterers: 19758 At special positions: 0 Unit cell: (120.35, 97.875, 128.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 89 16.00 O 3685 8.00 N 3497 7.00 C 12487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 913.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 33 sheets defined 33.3% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 7 through 26 removed outlier: 3.689A pdb=" N ASN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 4.252A pdb=" N HIS A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.550A pdb=" N ASN A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'C' and resid 7 through 26 Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.333A pdb=" N HIS C 31 " --> pdb=" O ASP C 28 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 32 " --> pdb=" O MET C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'D' and resid 7 through 26 Processing helix chain 'D' and resid 27 through 34 removed outlier: 4.493A pdb=" N HIS D 31 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 100 through 103 Processing helix chain 'B' and resid 7 through 26 removed outlier: 4.348A pdb=" N ASN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 34 removed outlier: 4.517A pdb=" N HIS B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'L' and resid 481 through 487 Processing helix chain 'L' and resid 499 through 506 Processing helix chain 'I' and resid 481 through 488 Processing helix chain 'I' and resid 499 through 507 Processing helix chain 'P' and resid 7 through 26 Processing helix chain 'P' and resid 27 through 33 removed outlier: 4.226A pdb=" N HIS P 31 " --> pdb=" O ASP P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 68 Processing helix chain 'P' and resid 86 through 88 No H-bonds generated for 'chain 'P' and resid 86 through 88' Processing helix chain 'N' and resid 7 through 26 Processing helix chain 'N' and resid 27 through 32 removed outlier: 4.268A pdb=" N HIS N 31 " --> pdb=" O ASP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 69 Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'N' and resid 134 through 138 Processing helix chain 'M' and resid 7 through 26 Processing helix chain 'M' and resid 27 through 32 removed outlier: 4.569A pdb=" N HIS M 31 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 69 Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'O' and resid 7 through 26 Processing helix chain 'O' and resid 27 through 34 removed outlier: 4.482A pdb=" N HIS O 31 " --> pdb=" O ASP O 28 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG O 32 " --> pdb=" O MET O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 86 through 88 No H-bonds generated for 'chain 'O' and resid 86 through 88' Processing helix chain 'V' and resid 481 through 487 Processing helix chain 'V' and resid 499 through 506 Processing helix chain 'U' and resid 481 through 488 Processing helix chain 'U' and resid 499 through 508 removed outlier: 3.998A pdb=" N LEU U 504 " --> pdb=" O GLU U 500 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR U 505 " --> pdb=" O VAL U 501 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP U 508 " --> pdb=" O LEU U 504 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 26 removed outlier: 3.805A pdb=" N ASN T 24 " --> pdb=" O TYR T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.272A pdb=" N HIS T 31 " --> pdb=" O ASP T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 69 removed outlier: 3.648A pdb=" N ASN T 69 " --> pdb=" O VAL T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 88 No H-bonds generated for 'chain 'T' and resid 86 through 88' Processing helix chain 'R' and resid 7 through 26 removed outlier: 3.775A pdb=" N ASN R 24 " --> pdb=" O TYR R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 32 removed outlier: 4.199A pdb=" N HIS R 31 " --> pdb=" O ASP R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 69 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'Q' and resid 7 through 26 Processing helix chain 'Q' and resid 27 through 34 removed outlier: 4.649A pdb=" N HIS Q 31 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 69 Processing helix chain 'S' and resid 7 through 26 removed outlier: 4.259A pdb=" N ASN S 24 " --> pdb=" O TYR S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 34 removed outlier: 4.488A pdb=" N HIS S 31 " --> pdb=" O ASP S 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG S 32 " --> pdb=" O MET S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 69 Processing helix chain 'X' and resid 481 through 487 Processing helix chain 'X' and resid 499 through 505 Processing helix chain 'W' and resid 481 through 488 Processing helix chain 'W' and resid 499 through 506 Processing helix chain 'E' and resid 7 through 26 removed outlier: 3.854A pdb=" N ASN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 removed outlier: 4.252A pdb=" N HIS E 31 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 32 " --> pdb=" O MET E 29 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR E 34 " --> pdb=" O HIS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 69 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 100 through 103 Processing helix chain 'G' and resid 7 through 26 Processing helix chain 'G' and resid 27 through 32 removed outlier: 4.169A pdb=" N HIS G 31 " --> pdb=" O ASP G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'H' and resid 7 through 26 Processing helix chain 'H' and resid 27 through 32 removed outlier: 4.534A pdb=" N HIS H 31 " --> pdb=" O ASP H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 69 Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'F' and resid 7 through 26 Processing helix chain 'F' and resid 27 through 34 removed outlier: 4.545A pdb=" N HIS F 31 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'J' and resid 481 through 488 removed outlier: 3.979A pdb=" N SER J 488 " --> pdb=" O GLU J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 508 removed outlier: 3.821A pdb=" N ASP J 508 " --> pdb=" O LEU J 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 488 Processing helix chain 'K' and resid 499 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 40 removed outlier: 11.095A pdb=" N GLY A 35 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N TYR A 125 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N ASN A 37 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS A 127 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL A 126 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 115 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 97 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE A 77 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER A 99 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N THR A 75 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 40 removed outlier: 11.095A pdb=" N GLY A 35 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N TYR A 125 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N ASN A 37 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N HIS A 127 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 56 removed outlier: 10.620A pdb=" N GLY C 35 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N TYR C 125 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN C 37 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS C 127 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 126 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 115 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 96 " --> pdb=" O PHE C 108 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 97 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE C 77 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER C 99 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR C 75 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 56 removed outlier: 10.620A pdb=" N GLY C 35 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N TYR C 125 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ASN C 37 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N HIS C 127 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 56 removed outlier: 5.628A pdb=" N VAL D 126 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA D 115 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 91 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 82 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN D 93 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 80 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET D 95 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.594A pdb=" N VAL B 41 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR B 133 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 126 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 115 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 97 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE B 77 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER B 99 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR B 75 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.594A pdb=" N VAL B 41 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N TYR B 133 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 124 " --> pdb=" O THR I 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'L' and resid 474 through 475 removed outlier: 6.882A pdb=" N THR L 474 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N VAL H 126 " --> pdb=" O THR L 474 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N GLY H 35 " --> pdb=" O LYS H 123 " (cutoff:3.500A) removed outlier: 9.787A pdb=" N TYR H 125 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N ASN H 37 " --> pdb=" O TYR H 125 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N HIS H 127 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 474 through 475 removed outlier: 6.882A pdb=" N THR L 474 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N VAL H 126 " --> pdb=" O THR L 474 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL H 126 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA H 115 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU H 97 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE H 77 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER H 99 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR H 75 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 39 through 40 removed outlier: 6.538A pdb=" N VAL P 113 " --> pdb=" O HIS P 127 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASP P 129 " --> pdb=" O THR P 111 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR P 111 " --> pdb=" O ASP P 129 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE P 131 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET P 109 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR P 133 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ARG P 107 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU P 97 " --> pdb=" O ILE P 77 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE P 77 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N SER P 99 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR P 75 " --> pdb=" O SER P 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 39 through 40 Processing sheet with id=AB4, first strand: chain 'N' and resid 55 through 56 removed outlier: 10.533A pdb=" N GLY N 35 " --> pdb=" O LYS N 123 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N TYR N 125 " --> pdb=" O GLY N 35 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ASN N 37 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS N 127 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL N 126 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA N 115 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG N 106 " --> pdb=" O LEU N 98 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY N 96 " --> pdb=" O PHE N 108 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU N 97 " --> pdb=" O ILE N 77 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE N 77 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER N 99 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N THR N 75 " --> pdb=" O SER N 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 55 through 56 removed outlier: 10.533A pdb=" N GLY N 35 " --> pdb=" O LYS N 123 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N TYR N 125 " --> pdb=" O GLY N 35 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N ASN N 37 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS N 127 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 55 through 56 removed outlier: 11.069A pdb=" N GLY M 35 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N TYR M 125 " --> pdb=" O GLY M 35 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N ASN M 37 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N HIS M 127 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL M 113 " --> pdb=" O HIS M 127 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP M 129 " --> pdb=" O THR M 111 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR M 111 " --> pdb=" O ASP M 129 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE M 131 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET M 109 " --> pdb=" O PHE M 131 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR M 133 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ARG M 107 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU M 97 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE M 77 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER M 99 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR M 75 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 55 through 56 removed outlier: 11.069A pdb=" N GLY M 35 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N TYR M 125 " --> pdb=" O GLY M 35 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N ASN M 37 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N HIS M 127 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 55 through 56 removed outlier: 3.594A pdb=" N ASP O 129 " --> pdb=" O SER O 39 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL O 126 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA O 115 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU O 97 " --> pdb=" O ILE O 77 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE O 77 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N SER O 99 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N THR O 75 " --> pdb=" O SER O 99 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 55 through 56 removed outlier: 3.594A pdb=" N ASP O 129 " --> pdb=" O SER O 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 474 through 475 removed outlier: 7.511A pdb=" N THR V 474 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N VAL Q 126 " --> pdb=" O THR V 474 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 474 through 475 removed outlier: 7.511A pdb=" N THR V 474 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N VAL Q 126 " --> pdb=" O THR V 474 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 115 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA Q 115 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU Q 97 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE Q 77 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N SER Q 99 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR Q 75 " --> pdb=" O SER Q 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 34 through 40 removed outlier: 11.051A pdb=" N GLY T 35 " --> pdb=" O LYS T 123 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N TYR T 125 " --> pdb=" O GLY T 35 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N ASN T 37 " --> pdb=" O TYR T 125 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS T 127 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL T 113 " --> pdb=" O HIS T 127 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP T 129 " --> pdb=" O THR T 111 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR T 111 " --> pdb=" O ASP T 129 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE T 131 " --> pdb=" O MET T 109 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET T 109 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR T 133 " --> pdb=" O ARG T 107 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ARG T 107 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU T 97 " --> pdb=" O ILE T 77 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ILE T 77 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER T 99 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR T 75 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 34 through 40 removed outlier: 11.051A pdb=" N GLY T 35 " --> pdb=" O LYS T 123 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N TYR T 125 " --> pdb=" O GLY T 35 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N ASN T 37 " --> pdb=" O TYR T 125 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS T 127 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE T 124 " --> pdb=" O THR X 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 55 through 56 removed outlier: 10.803A pdb=" N GLY R 35 " --> pdb=" O LYS R 123 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N TYR R 125 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN R 37 " --> pdb=" O TYR R 125 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N HIS R 127 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL R 126 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA R 115 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY R 96 " --> pdb=" O PHE R 108 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU R 97 " --> pdb=" O ILE R 77 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE R 77 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER R 99 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR R 75 " --> pdb=" O SER R 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 55 through 56 removed outlier: 10.803A pdb=" N GLY R 35 " --> pdb=" O LYS R 123 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N TYR R 125 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ASN R 37 " --> pdb=" O TYR R 125 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N HIS R 127 " --> pdb=" O ASN R 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 39 through 40 Processing sheet with id=AC8, first strand: chain 'S' and resid 74 through 85 removed outlier: 5.541A pdb=" N THR S 75 " --> pdb=" O SER S 99 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N SER S 99 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE S 77 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU S 97 " --> pdb=" O ILE S 77 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA S 115 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL S 126 " --> pdb=" O ALA S 115 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE S 124 " --> pdb=" O THR W 474 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 55 through 56 removed outlier: 6.491A pdb=" N VAL E 113 " --> pdb=" O HIS E 127 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP E 129 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR E 111 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE E 131 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET E 109 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR E 133 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG E 107 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU E 97 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE E 77 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER E 99 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N THR E 75 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 55 through 56 removed outlier: 3.697A pdb=" N PHE E 124 " --> pdb=" O THR J 492 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 55 through 56 removed outlier: 10.903A pdb=" N GLY G 35 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N TYR G 125 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N ASN G 37 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS G 127 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL G 126 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA G 115 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY G 96 " --> pdb=" O PHE G 108 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 97 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE G 77 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER G 99 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR G 75 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 55 through 56 removed outlier: 10.903A pdb=" N GLY G 35 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N TYR G 125 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N ASN G 37 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N HIS G 127 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.574A pdb=" N ASP F 46 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 74 through 84 removed outlier: 5.517A pdb=" N THR F 75 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER F 99 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE F 77 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 97 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA F 115 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL F 126 " --> pdb=" O ALA F 115 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2565 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: 3.43 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5535 1.33 - 1.46: 4165 1.46 - 1.58: 10360 1.58 - 1.70: 2 1.70 - 1.82: 161 Bond restraints: 20223 Sorted by residual: bond pdb=" N VAL C 55 " pdb=" CA VAL C 55 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.19e-02 7.06e+03 8.74e+00 bond pdb=" N HIS D 74 " pdb=" CA HIS D 74 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.66e+00 bond pdb=" N GLN H 25 " pdb=" CA GLN H 25 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 7.96e+00 bond pdb=" N PHE W 475 " pdb=" CA PHE W 475 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.29e-02 6.01e+03 7.86e+00 bond pdb=" N VAL P 91 " pdb=" CA VAL P 91 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.54e+00 ... (remaining 20218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 26443 2.45 - 4.89: 801 4.89 - 7.34: 75 7.34 - 9.78: 26 9.78 - 12.23: 6 Bond angle restraints: 27351 Sorted by residual: angle pdb=" N LEU K 497 " pdb=" CA LEU K 497 " pdb=" C LEU K 497 " ideal model delta sigma weight residual 110.20 102.03 8.17 1.44e+00 4.82e-01 3.22e+01 angle pdb=" CA LEU K 497 " pdb=" C LEU K 497 " pdb=" N PRO K 498 " ideal model delta sigma weight residual 117.44 123.45 -6.01 1.13e+00 7.83e-01 2.83e+01 angle pdb=" C SER F 47 " pdb=" CA SER F 47 " pdb=" CB SER F 47 " ideal model delta sigma weight residual 117.23 110.12 7.11 1.36e+00 5.41e-01 2.74e+01 angle pdb=" N GLU L 484 " pdb=" CA GLU L 484 " pdb=" C GLU L 484 " ideal model delta sigma weight residual 111.36 106.07 5.29 1.09e+00 8.42e-01 2.36e+01 angle pdb=" N GLN R 103 " pdb=" CA GLN R 103 " pdb=" C GLN R 103 " ideal model delta sigma weight residual 109.80 101.55 8.25 1.70e+00 3.46e-01 2.36e+01 ... (remaining 27346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10319 17.87 - 35.73: 1286 35.73 - 53.59: 302 53.59 - 71.46: 27 71.46 - 89.32: 19 Dihedral angle restraints: 11953 sinusoidal: 4833 harmonic: 7120 Sorted by residual: dihedral pdb=" CA GLN D 68 " pdb=" C GLN D 68 " pdb=" N ASN D 69 " pdb=" CA ASN D 69 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLN M 68 " pdb=" C GLN M 68 " pdb=" N ASN M 69 " pdb=" CA ASN M 69 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA VAL N 55 " pdb=" C VAL N 55 " pdb=" N TYR N 56 " pdb=" CA TYR N 56 " ideal model delta harmonic sigma weight residual -180.00 -156.09 -23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 11950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2386 0.070 - 0.140: 448 0.140 - 0.211: 62 0.211 - 0.281: 3 0.281 - 0.351: 6 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA LEU K 497 " pdb=" N LEU K 497 " pdb=" C LEU K 497 " pdb=" CB LEU K 497 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ASN C 102 " pdb=" N ASN C 102 " pdb=" C ASN C 102 " pdb=" CB ASN C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ASP W 477 " pdb=" N ASP W 477 " pdb=" C ASP W 477 " pdb=" CB ASP W 477 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2902 not shown) Planarity restraints: 3638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN Q 68 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C GLN Q 68 " -0.065 2.00e-02 2.50e+03 pdb=" O GLN Q 68 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN Q 69 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 26 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO R 27 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO R 27 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO R 27 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR T 75 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C THR T 75 " -0.059 2.00e-02 2.50e+03 pdb=" O THR T 75 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS T 76 " 0.020 2.00e-02 2.50e+03 ... (remaining 3635 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1331 2.74 - 3.28: 19995 3.28 - 3.82: 33439 3.82 - 4.36: 40205 4.36 - 4.90: 70031 Nonbonded interactions: 165001 Sorted by model distance: nonbonded pdb=" OH TYR N 34 " pdb=" OD2 ASP N 129 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR F 20 " pdb=" OE1 GLN F 110 " model vdw 2.203 3.040 nonbonded pdb=" NZ LYS S 123 " pdb=" OG1 THR W 474 " model vdw 2.205 3.120 nonbonded pdb=" OH TYR P 34 " pdb=" OD2 ASP P 129 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR N 20 " pdb=" OE1 GLN N 110 " model vdw 2.228 3.040 ... (remaining 164996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'B' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'C' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'D' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'E' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'F' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'G' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'H' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'M' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'N' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'O' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'P' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'Q' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'R' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'S' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'T' and (resid 5 through 72 or resid 74 through 138)) } ncs_group { reference = (chain 'I' and resid 472 through 508) selection = chain 'J' selection = (chain 'K' and resid 472 through 508) selection = chain 'L' selection = (chain 'U' and resid 472 through 508) selection = chain 'V' selection = (chain 'W' and resid 472 through 508) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.220 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 20223 Z= 0.326 Angle : 0.919 12.225 27351 Z= 0.559 Chirality : 0.057 0.351 2905 Planarity : 0.005 0.087 3638 Dihedral : 16.129 89.325 7383 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.53 % Allowed : 29.53 % Favored : 68.94 % Cbeta Deviations : 0.04 % 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: 1.18 (0.18), residues: 2415 helix: 1.65 (0.20), residues: 652 sheet: 0.08 (0.18), residues: 738 loop : 1.00 (0.24), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 32 TYR 0.023 0.001 TYR N 40 PHE 0.020 0.002 PHE D 112 TRP 0.005 0.001 TRP W 509 HIS 0.006 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00512 (20223) covalent geometry : angle 0.91868 (27351) hydrogen bonds : bond 0.11616 ( 909) hydrogen bonds : angle 6.13908 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 649 time to evaluate : 0.920 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: C 88 ASP cc_start: 0.8501 (t0) cc_final: 0.8261 (t0) REVERT: C 107 ARG cc_start: 0.7248 (ttm170) cc_final: 0.6815 (ttm170) REVERT: D 134 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: B 50 LYS cc_start: 0.8906 (pttt) cc_final: 0.8592 (pmtt) REVERT: B 53 ASP cc_start: 0.9002 (p0) cc_final: 0.8756 (p0) REVERT: P 81 ASP cc_start: 0.7891 (m-30) cc_final: 0.7116 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9365 (m-40) cc_final: 0.9141 (m110) REVERT: P 88 ASP cc_start: 0.8645 (m-30) cc_final: 0.8084 (t0) REVERT: M 76 LYS cc_start: 0.8400 (mtpt) cc_final: 0.8177 (mttt) REVERT: M 78 ARG cc_start: 0.8260 (mpt180) cc_final: 0.8025 (tpp-160) REVERT: M 88 ASP cc_start: 0.9066 (m-30) cc_final: 0.8858 (t0) REVERT: O 53 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8913 (p0) REVERT: O 95 MET cc_start: 0.7725 (mtm) cc_final: 0.7259 (mtp) REVERT: T 53 ASP cc_start: 0.8786 (p0) cc_final: 0.8526 (p0) REVERT: R 62 HIS cc_start: 0.8227 (t70) cc_final: 0.8025 (t-90) REVERT: R 63 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8614 (ttp80) REVERT: R 74 HIS cc_start: 0.7223 (m-70) cc_final: 0.7000 (m170) REVERT: Q 13 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8364 (mmm-85) REVERT: Q 69 ASN cc_start: 0.7379 (t0) cc_final: 0.7068 (t0) REVERT: S 53 ASP cc_start: 0.8962 (p0) cc_final: 0.8750 (p0) REVERT: W 500 GLU cc_start: 0.8320 (tt0) cc_final: 0.7971 (mt-10) REVERT: G 3 MET cc_start: 0.7219 (tpp) cc_final: 0.6803 (tpp) REVERT: G 69 ASN cc_start: 0.8705 (p0) cc_final: 0.8203 (p0) REVERT: G 74 HIS cc_start: 0.7159 (m-70) cc_final: 0.6959 (m170) REVERT: H 88 ASP cc_start: 0.9100 (m-30) cc_final: 0.8712 (t0) REVERT: H 133 TYR cc_start: 0.8283 (m-80) cc_final: 0.8054 (m-80) REVERT: F 53 ASP cc_start: 0.8905 (p0) cc_final: 0.8653 (p0) REVERT: F 59 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8863 (mptt) REVERT: F 109 MET cc_start: 0.7890 (mmt) cc_final: 0.7108 (mmt) outliers start: 33 outliers final: 23 residues processed: 671 average time/residue: 0.6306 time to fit residues: 475.0598 Evaluate side-chains 587 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 563 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 69 ASN Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 128 ASN C 24 ASN C 62 HIS ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 72 ASN D 134 GLN B 102 ASN B 110 GLN ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN P 128 ASN N 74 HIS N 101 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN O 68 GLN T 68 GLN T 103 GLN T 110 GLN T 128 ASN R 72 ASN R 101 ASN S 37 ASN E 24 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 127 HIS E 128 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN F 24 ASN F 37 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.125294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098788 restraints weight = 60812.723| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 5.09 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20223 Z= 0.162 Angle : 0.653 10.500 27351 Z= 0.332 Chirality : 0.046 0.198 2905 Planarity : 0.004 0.059 3638 Dihedral : 5.714 66.598 2741 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.47 % Allowed : 27.17 % Favored : 67.36 % 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 (0.19), residues: 2415 helix: 1.97 (0.20), residues: 656 sheet: 0.12 (0.18), residues: 758 loop : 1.29 (0.24), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 17 TYR 0.022 0.001 TYR N 40 PHE 0.026 0.002 PHE M 70 TRP 0.016 0.001 TRP I 509 HIS 0.005 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00377 (20223) covalent geometry : angle 0.65305 (27351) hydrogen bonds : bond 0.03718 ( 909) hydrogen bonds : angle 5.06405 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 619 time to evaluate : 0.776 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 68 GLN cc_start: 0.8319 (mm110) cc_final: 0.8049 (mm-40) REVERT: A 103 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: C 14 GLU cc_start: 0.7268 (tp30) cc_final: 0.6894 (tp30) REVERT: C 63 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8687 (tmm-80) REVERT: C 103 GLN cc_start: 0.8905 (mm110) cc_final: 0.8551 (mm110) REVERT: D 13 ARG cc_start: 0.8702 (mmt90) cc_final: 0.8322 (mmm-85) REVERT: D 17 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8569 (ttp80) REVERT: D 32 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8681 (mmm-85) REVERT: D 81 ASP cc_start: 0.7669 (m-30) cc_final: 0.7391 (m-30) REVERT: D 134 GLN cc_start: 0.7338 (tm-30) cc_final: 0.7122 (tm-30) REVERT: B 14 GLU cc_start: 0.7582 (tp30) cc_final: 0.7331 (tp30) REVERT: B 46 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7020 (OUTLIER) REVERT: B 50 LYS cc_start: 0.8895 (pttt) cc_final: 0.8610 (pmtt) REVERT: B 53 ASP cc_start: 0.8988 (p0) cc_final: 0.8765 (p0) REVERT: P 29 MET cc_start: 0.8294 (mmp) cc_final: 0.8057 (mmm) REVERT: P 81 ASP cc_start: 0.7672 (m-30) cc_final: 0.7159 (t0) REVERT: P 87 ASN cc_start: 0.9371 (m-40) cc_final: 0.9091 (m110) REVERT: P 88 ASP cc_start: 0.8635 (m-30) cc_final: 0.8104 (t0) REVERT: N 14 GLU cc_start: 0.7117 (tp30) cc_final: 0.6730 (tp30) REVERT: N 103 GLN cc_start: 0.8521 (mm110) cc_final: 0.8230 (mm-40) REVERT: M 29 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7781 (mtt) REVERT: M 68 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7952 (pp30) REVERT: M 76 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8301 (mttt) REVERT: M 88 ASP cc_start: 0.9086 (m-30) cc_final: 0.8786 (t0) REVERT: O 14 GLU cc_start: 0.7793 (tp30) cc_final: 0.7389 (tp30) REVERT: O 50 LYS cc_start: 0.8411 (pptt) cc_final: 0.8140 (mmmt) REVERT: O 53 ASP cc_start: 0.8998 (p0) cc_final: 0.8793 (p0) REVERT: V 474 THR cc_start: 0.8444 (p) cc_final: 0.8046 (t) REVERT: U 500 GLU cc_start: 0.8599 (tt0) cc_final: 0.8335 (tt0) REVERT: T 14 GLU cc_start: 0.8314 (tp30) cc_final: 0.7651 (tp30) REVERT: T 53 ASP cc_start: 0.8745 (p0) cc_final: 0.8538 (p0) REVERT: T 76 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7854 (tptt) REVERT: R 14 GLU cc_start: 0.7137 (tp30) cc_final: 0.6779 (tp30) REVERT: R 36 LYS cc_start: 0.8737 (mptt) cc_final: 0.8405 (mppt) REVERT: R 62 HIS cc_start: 0.8238 (t70) cc_final: 0.8015 (t-90) REVERT: R 72 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7268 (p0) REVERT: R 103 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7717 (mm-40) REVERT: Q 14 GLU cc_start: 0.9001 (tp30) cc_final: 0.8709 (tp30) REVERT: Q 17 ARG cc_start: 0.8716 (ttp80) cc_final: 0.8325 (ttp80) REVERT: Q 68 GLN cc_start: 0.8161 (tp40) cc_final: 0.7811 (tp40) REVERT: Q 69 ASN cc_start: 0.7341 (t0) cc_final: 0.7025 (t0) REVERT: S 14 GLU cc_start: 0.7710 (tp30) cc_final: 0.7338 (tp30) REVERT: S 46 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6743 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8842 (pptt) cc_final: 0.8426 (pmtt) REVERT: S 53 ASP cc_start: 0.8919 (p0) cc_final: 0.8687 (p0) REVERT: S 109 MET cc_start: 0.7530 (mmt) cc_final: 0.7082 (mmt) REVERT: X 502 ASP cc_start: 0.8779 (m-30) cc_final: 0.8375 (m-30) REVERT: X 504 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7932 (mp) REVERT: W 500 GLU cc_start: 0.8539 (tt0) cc_final: 0.8186 (mt-10) REVERT: E 5 LYS cc_start: 0.9163 (mtpm) cc_final: 0.8934 (tttp) REVERT: G 1 MET cc_start: 0.6154 (ttt) cc_final: 0.5807 (ttt) REVERT: G 3 MET cc_start: 0.7311 (tpp) cc_final: 0.6890 (tpp) REVERT: G 14 GLU cc_start: 0.7172 (tp30) cc_final: 0.6794 (tp30) REVERT: G 32 ARG cc_start: 0.8766 (mtm180) cc_final: 0.8396 (mtp180) REVERT: G 103 GLN cc_start: 0.8431 (mm110) cc_final: 0.8093 (mm110) REVERT: H 29 MET cc_start: 0.8325 (mtp) cc_final: 0.8071 (mtt) REVERT: H 88 ASP cc_start: 0.9135 (m-30) cc_final: 0.8647 (t0) REVERT: F 14 GLU cc_start: 0.7661 (tp30) cc_final: 0.7385 (tp30) REVERT: F 53 ASP cc_start: 0.8898 (p0) cc_final: 0.8667 (p0) REVERT: F 59 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8866 (mptt) REVERT: J 500 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7765 (pt0) outliers start: 118 outliers final: 47 residues processed: 677 average time/residue: 0.6148 time to fit residues: 468.0517 Evaluate side-chains 610 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 556 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 132 ARG Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 506 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 73 CYS Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 36 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 24 ASN C 37 ASN C 72 ASN C 74 HIS D 37 ASN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN N 68 GLN N 72 ASN M 18 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN O 93 GLN T 31 HIS T 68 GLN T 103 GLN T 110 GLN R 48 ASN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 HIS ** R 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 69 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 HIS S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 37 ASN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 ASN F 37 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.122992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096898 restraints weight = 55380.668| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.86 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20223 Z= 0.180 Angle : 0.653 9.842 27351 Z= 0.330 Chirality : 0.046 0.190 2905 Planarity : 0.004 0.055 3638 Dihedral : 5.152 61.932 2710 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.47 % Allowed : 27.49 % Favored : 67.04 % 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: 1.56 (0.19), residues: 2415 helix: 2.24 (0.20), residues: 636 sheet: 0.10 (0.18), residues: 762 loop : 1.25 (0.24), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 63 TYR 0.019 0.001 TYR G 20 PHE 0.019 0.002 PHE H 15 TRP 0.010 0.001 TRP I 509 HIS 0.004 0.001 HIS A 79 Details of bonding type rmsd covalent geometry : bond 0.00420 (20223) covalent geometry : angle 0.65341 (27351) hydrogen bonds : bond 0.03717 ( 909) hydrogen bonds : angle 4.94560 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 607 time to evaluate : 0.741 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 5 LYS cc_start: 0.8712 (mtpm) cc_final: 0.8457 (mtpt) REVERT: A 29 MET cc_start: 0.8570 (mmp) cc_final: 0.8315 (mmp) REVERT: A 88 ASP cc_start: 0.8004 (t0) cc_final: 0.7746 (t0) REVERT: C 14 GLU cc_start: 0.7339 (tp30) cc_final: 0.6932 (tp30) REVERT: C 88 ASP cc_start: 0.8369 (t0) cc_final: 0.8104 (t0) REVERT: C 101 ASN cc_start: 0.8866 (m-40) cc_final: 0.8565 (m110) REVERT: C 103 GLN cc_start: 0.8924 (mm110) cc_final: 0.8477 (mm-40) REVERT: D 13 ARG cc_start: 0.8725 (mmt90) cc_final: 0.8331 (mmm-85) REVERT: D 14 GLU cc_start: 0.9029 (tp30) cc_final: 0.8811 (tp30) REVERT: D 17 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8544 (ttp80) REVERT: D 32 ARG cc_start: 0.9158 (mmm-85) cc_final: 0.8895 (mmm-85) REVERT: B 14 GLU cc_start: 0.7706 (tp30) cc_final: 0.7440 (tp30) REVERT: B 50 LYS cc_start: 0.8899 (pttt) cc_final: 0.8657 (mmmt) REVERT: B 53 ASP cc_start: 0.9009 (p0) cc_final: 0.8808 (p0) REVERT: B 66 MET cc_start: 0.8536 (mmm) cc_final: 0.8300 (mmm) REVERT: B 109 MET cc_start: 0.8253 (mmt) cc_final: 0.7882 (mmt) REVERT: P 68 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7218 (mt0) REVERT: P 81 ASP cc_start: 0.7713 (m-30) cc_final: 0.7209 (t0) REVERT: P 87 ASN cc_start: 0.9383 (m-40) cc_final: 0.9155 (m-40) REVERT: P 103 GLN cc_start: 0.8727 (mm110) cc_final: 0.8458 (mt0) REVERT: P 132 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7575 (mmt-90) REVERT: N 14 GLU cc_start: 0.7189 (tp30) cc_final: 0.6741 (tp30) REVERT: N 60 GLU cc_start: 0.6825 (pp20) cc_final: 0.6606 (pp20) REVERT: N 68 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: N 103 GLN cc_start: 0.8688 (mm110) cc_final: 0.8312 (mm-40) REVERT: M 29 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7796 (mtt) REVERT: M 68 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: M 88 ASP cc_start: 0.9077 (m-30) cc_final: 0.8741 (t0) REVERT: M 109 MET cc_start: 0.7980 (ptm) cc_final: 0.7680 (ttt) REVERT: O 14 GLU cc_start: 0.7812 (tp30) cc_final: 0.7567 (tp30) REVERT: O 66 MET cc_start: 0.8472 (mmm) cc_final: 0.8232 (mmm) REVERT: O 95 MET cc_start: 0.8834 (mtm) cc_final: 0.7609 (mtp) REVERT: V 474 THR cc_start: 0.8490 (p) cc_final: 0.8036 (t) REVERT: T 14 GLU cc_start: 0.8368 (tp30) cc_final: 0.7700 (tp30) REVERT: T 53 ASP cc_start: 0.8743 (p0) cc_final: 0.8541 (p0) REVERT: T 76 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7841 (tptt) REVERT: R 14 GLU cc_start: 0.7242 (tp30) cc_final: 0.6850 (tp30) REVERT: R 36 LYS cc_start: 0.8781 (mptt) cc_final: 0.8407 (mppt) REVERT: R 103 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7921 (mp10) REVERT: Q 17 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8522 (ttp80) REVERT: Q 29 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8124 (mtp) REVERT: Q 68 GLN cc_start: 0.8251 (tp40) cc_final: 0.7882 (tp40) REVERT: S 14 GLU cc_start: 0.7757 (tp30) cc_final: 0.7326 (tp30) REVERT: S 46 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6657 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8826 (pptt) cc_final: 0.8382 (pmtt) REVERT: S 53 ASP cc_start: 0.8989 (p0) cc_final: 0.8766 (p0) REVERT: S 66 MET cc_start: 0.8585 (mmm) cc_final: 0.8366 (mmm) REVERT: S 109 MET cc_start: 0.7640 (mmt) cc_final: 0.7110 (mmt) REVERT: S 110 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: X 504 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7954 (mp) REVERT: W 500 GLU cc_start: 0.8508 (tt0) cc_final: 0.8194 (mt-10) REVERT: E 5 LYS cc_start: 0.9140 (mtpm) cc_final: 0.8905 (tttp) REVERT: E 36 LYS cc_start: 0.9011 (tppp) cc_final: 0.8807 (tppp) REVERT: E 103 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: G 3 MET cc_start: 0.7451 (tpp) cc_final: 0.7050 (tpp) REVERT: G 14 GLU cc_start: 0.7198 (tp30) cc_final: 0.6782 (tp30) REVERT: G 95 MET cc_start: 0.8844 (mtp) cc_final: 0.8612 (mtp) REVERT: G 103 GLN cc_start: 0.8668 (mm110) cc_final: 0.8268 (mp10) REVERT: H 88 ASP cc_start: 0.9114 (m-30) cc_final: 0.8598 (t0) REVERT: H 117 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7984 (mt-10) REVERT: F 32 ARG cc_start: 0.8490 (mtp180) cc_final: 0.8187 (mtp180) REVERT: F 53 ASP cc_start: 0.8963 (p0) cc_final: 0.8752 (p0) REVERT: J 477 ASP cc_start: 0.8786 (p0) cc_final: 0.8582 (p0) REVERT: J 500 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7917 (pt0) outliers start: 118 outliers final: 52 residues processed: 662 average time/residue: 0.6409 time to fit residues: 477.1066 Evaluate side-chains 624 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 562 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 483 ILE Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 95 MET Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 500 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN D 68 GLN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN N 24 ASN N 72 ASN N 74 HIS ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS T 68 GLN T 110 GLN R 68 GLN R 72 ASN R 74 HIS R 101 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 100 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS G 101 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.118358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092900 restraints weight = 57865.668| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 4.81 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20223 Z= 0.261 Angle : 0.695 10.691 27351 Z= 0.355 Chirality : 0.048 0.242 2905 Planarity : 0.004 0.050 3638 Dihedral : 5.369 57.567 2710 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 7.05 % Allowed : 26.89 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.42 (0.18), residues: 2415 helix: 2.09 (0.20), residues: 636 sheet: 0.02 (0.18), residues: 762 loop : 1.18 (0.23), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 63 TYR 0.020 0.002 TYR N 40 PHE 0.024 0.002 PHE D 15 TRP 0.008 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00606 (20223) covalent geometry : angle 0.69536 (27351) hydrogen bonds : bond 0.04090 ( 909) hydrogen bonds : angle 5.05619 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 594 time to evaluate : 0.806 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: A 68 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8086 (mm-40) REVERT: A 88 ASP cc_start: 0.8281 (t0) cc_final: 0.8059 (t0) REVERT: A 134 GLN cc_start: 0.7632 (tt0) cc_final: 0.7375 (tt0) REVERT: C 14 GLU cc_start: 0.7345 (tp30) cc_final: 0.6977 (tp30) REVERT: C 88 ASP cc_start: 0.8504 (t0) cc_final: 0.8285 (t0) REVERT: C 103 GLN cc_start: 0.8932 (mm110) cc_final: 0.8291 (mp10) REVERT: C 109 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: D 13 ARG cc_start: 0.8723 (mmt90) cc_final: 0.8328 (mmm-85) REVERT: D 14 GLU cc_start: 0.9018 (tp30) cc_final: 0.8707 (tp30) REVERT: D 17 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8550 (tmm-80) REVERT: D 25 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: D 29 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8038 (mtp) REVERT: D 81 ASP cc_start: 0.7654 (m-30) cc_final: 0.7302 (m-30) REVERT: D 133 TYR cc_start: 0.8825 (m-80) cc_final: 0.8609 (m-80) REVERT: B 14 GLU cc_start: 0.7728 (tp30) cc_final: 0.7382 (tp30) REVERT: B 50 LYS cc_start: 0.8845 (pttt) cc_final: 0.8627 (mmmt) REVERT: B 66 MET cc_start: 0.8636 (mmm) cc_final: 0.8335 (mmm) REVERT: B 109 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7923 (mmt) REVERT: P 68 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7297 (mt0) REVERT: P 87 ASN cc_start: 0.9357 (m-40) cc_final: 0.9114 (m-40) REVERT: P 103 GLN cc_start: 0.8725 (mm110) cc_final: 0.8432 (mt0) REVERT: P 132 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7685 (mmt-90) REVERT: N 14 GLU cc_start: 0.7192 (tp30) cc_final: 0.6761 (tp30) REVERT: N 103 GLN cc_start: 0.8796 (mm110) cc_final: 0.8319 (mp10) REVERT: M 14 GLU cc_start: 0.8984 (tp30) cc_final: 0.8644 (tp30) REVERT: M 17 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8599 (ttp80) REVERT: M 29 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7904 (mtt) REVERT: M 68 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: M 88 ASP cc_start: 0.9123 (m-30) cc_final: 0.8778 (t0) REVERT: O 14 GLU cc_start: 0.7742 (tp30) cc_final: 0.7471 (tp30) REVERT: O 66 MET cc_start: 0.8598 (mmm) cc_final: 0.8293 (mmm) REVERT: O 95 MET cc_start: 0.8834 (mtm) cc_final: 0.8272 (mtp) REVERT: T 14 GLU cc_start: 0.8383 (tp30) cc_final: 0.7673 (tp30) REVERT: T 53 ASP cc_start: 0.8825 (p0) cc_final: 0.8602 (p0) REVERT: T 76 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7824 (tptt) REVERT: T 88 ASP cc_start: 0.8421 (t0) cc_final: 0.8218 (t0) REVERT: R 14 GLU cc_start: 0.7190 (tp30) cc_final: 0.6812 (tp30) REVERT: R 36 LYS cc_start: 0.8845 (mptt) cc_final: 0.8455 (mppt) REVERT: R 88 ASP cc_start: 0.8522 (t0) cc_final: 0.8254 (t0) REVERT: R 103 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7996 (mp10) REVERT: Q 25 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: Q 29 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8110 (mtp) REVERT: Q 109 MET cc_start: 0.8396 (ttp) cc_final: 0.8108 (ttm) REVERT: S 14 GLU cc_start: 0.7710 (tp30) cc_final: 0.7351 (tp30) REVERT: S 46 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6624 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8814 (pptt) cc_final: 0.8345 (pmtt) REVERT: S 66 MET cc_start: 0.8659 (mmm) cc_final: 0.8349 (mmm) REVERT: S 109 MET cc_start: 0.7889 (mmt) cc_final: 0.7383 (mmt) REVERT: S 110 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: X 504 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7993 (mp) REVERT: W 500 GLU cc_start: 0.8515 (tt0) cc_final: 0.8231 (mt-10) REVERT: E 5 LYS cc_start: 0.9094 (mtpm) cc_final: 0.8798 (tttp) REVERT: E 103 GLN cc_start: 0.8572 (mm-40) cc_final: 0.7980 (mt0) REVERT: G 3 MET cc_start: 0.7734 (tpp) cc_final: 0.7330 (tpp) REVERT: G 14 GLU cc_start: 0.7187 (tp30) cc_final: 0.6788 (tp30) REVERT: G 103 GLN cc_start: 0.8758 (mm110) cc_final: 0.8343 (mp10) REVERT: G 109 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7741 (mtt) REVERT: H 29 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8034 (mtp) REVERT: H 88 ASP cc_start: 0.9116 (m-30) cc_final: 0.8616 (t0) REVERT: H 117 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8127 (mt-10) REVERT: F 76 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7607 (mtpt) REVERT: J 500 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (pt0) outliers start: 152 outliers final: 71 residues processed: 662 average time/residue: 0.6357 time to fit residues: 472.2104 Evaluate side-chains 630 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 543 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain L residue 483 ILE Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 109 MET Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain V residue 497 LEU Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain U residue 504 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain X residue 506 ASP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 HIS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 103 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 37 ASN C 74 HIS ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN M 18 GLN M 37 ASN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN R 37 ASN R 68 GLN R 72 ASN R 74 HIS R 101 ASN Q 68 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 102 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN G 37 ASN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.099268 restraints weight = 40566.503| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 4.11 r_work: 0.3362 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20223 Z= 0.139 Angle : 0.667 10.527 27351 Z= 0.334 Chirality : 0.046 0.238 2905 Planarity : 0.004 0.063 3638 Dihedral : 5.035 54.943 2710 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.19 % Allowed : 30.18 % Favored : 64.63 % 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: 1.57 (0.19), residues: 2415 helix: 2.20 (0.20), residues: 636 sheet: 0.17 (0.19), residues: 738 loop : 1.19 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 63 TYR 0.022 0.001 TYR N 40 PHE 0.024 0.002 PHE I 475 TRP 0.008 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00320 (20223) covalent geometry : angle 0.66698 (27351) hydrogen bonds : bond 0.03487 ( 909) hydrogen bonds : angle 4.88840 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 622 time to evaluate : 0.818 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 5 LYS cc_start: 0.8719 (mtpm) cc_final: 0.8474 (mtpt) REVERT: A 14 GLU cc_start: 0.8473 (tp30) cc_final: 0.7829 (tp30) REVERT: A 68 GLN cc_start: 0.8387 (mm110) cc_final: 0.8157 (mm-40) REVERT: A 88 ASP cc_start: 0.8281 (t0) cc_final: 0.7940 (t0) REVERT: A 134 GLN cc_start: 0.7690 (tt0) cc_final: 0.7364 (tt0) REVERT: C 14 GLU cc_start: 0.7524 (tp30) cc_final: 0.7119 (tp30) REVERT: C 88 ASP cc_start: 0.8392 (t0) cc_final: 0.8077 (t0) REVERT: C 101 ASN cc_start: 0.8930 (m-40) cc_final: 0.8578 (m110) REVERT: C 103 GLN cc_start: 0.9045 (mm110) cc_final: 0.8568 (mm-40) REVERT: C 109 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8175 (mtp) REVERT: D 17 ARG cc_start: 0.8885 (ttp80) cc_final: 0.8571 (ttp80) REVERT: D 29 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: D 93 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7666 (tm-30) REVERT: D 134 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 14 GLU cc_start: 0.8050 (tp30) cc_final: 0.7738 (tp30) REVERT: B 50 LYS cc_start: 0.8927 (pttt) cc_final: 0.8653 (mmmt) REVERT: B 66 MET cc_start: 0.8764 (mmm) cc_final: 0.8411 (mmm) REVERT: I 500 GLU cc_start: 0.8058 (tt0) cc_final: 0.7835 (tt0) REVERT: I 504 LEU cc_start: 0.8920 (mm) cc_final: 0.8716 (mp) REVERT: P 68 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: P 81 ASP cc_start: 0.8008 (m-30) cc_final: 0.7469 (t0) REVERT: P 87 ASN cc_start: 0.9382 (m-40) cc_final: 0.8940 (m-40) REVERT: P 88 ASP cc_start: 0.8852 (m-30) cc_final: 0.8026 (t0) REVERT: P 103 GLN cc_start: 0.8883 (mm110) cc_final: 0.8633 (mt0) REVERT: N 14 GLU cc_start: 0.7342 (tp30) cc_final: 0.6895 (tp30) REVERT: N 60 GLU cc_start: 0.7262 (pp20) cc_final: 0.6934 (pp20) REVERT: N 103 GLN cc_start: 0.8919 (mm110) cc_final: 0.8383 (mp10) REVERT: M 14 GLU cc_start: 0.8996 (tp30) cc_final: 0.8730 (tp30) REVERT: M 17 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8707 (ttp80) REVERT: M 29 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8347 (mtt) REVERT: M 32 ARG cc_start: 0.9063 (mmm-85) cc_final: 0.8769 (mmm-85) REVERT: M 68 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: M 88 ASP cc_start: 0.9212 (m-30) cc_final: 0.8836 (t0) REVERT: O 14 GLU cc_start: 0.8132 (tp30) cc_final: 0.7744 (tp30) REVERT: O 66 MET cc_start: 0.8717 (mmm) cc_final: 0.8366 (mmm) REVERT: O 95 MET cc_start: 0.9079 (mtm) cc_final: 0.8569 (mtp) REVERT: V 474 THR cc_start: 0.8442 (p) cc_final: 0.7824 (t) REVERT: T 5 LYS cc_start: 0.9003 (mtpm) cc_final: 0.8698 (ttmt) REVERT: T 14 GLU cc_start: 0.8617 (tp30) cc_final: 0.8018 (tp30) REVERT: T 53 ASP cc_start: 0.8815 (p0) cc_final: 0.8608 (p0) REVERT: T 87 ASN cc_start: 0.9119 (m-40) cc_final: 0.8779 (m110) REVERT: T 88 ASP cc_start: 0.8471 (t0) cc_final: 0.8197 (t0) REVERT: R 14 GLU cc_start: 0.7381 (tp30) cc_final: 0.7002 (tp30) REVERT: R 25 GLN cc_start: 0.8626 (mm-40) cc_final: 0.7994 (mm110) REVERT: R 36 LYS cc_start: 0.8887 (mptt) cc_final: 0.8478 (mppt) REVERT: R 88 ASP cc_start: 0.8417 (t0) cc_final: 0.8120 (t0) REVERT: Q 29 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8479 (mtp) REVERT: Q 68 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: S 14 GLU cc_start: 0.8126 (tp30) cc_final: 0.7706 (tp30) REVERT: S 46 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.6606 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8880 (pptt) cc_final: 0.8372 (pmtt) REVERT: S 66 MET cc_start: 0.8795 (mmm) cc_final: 0.8518 (mmm) REVERT: S 109 MET cc_start: 0.8206 (mmt) cc_final: 0.7866 (mmt) REVERT: X 504 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7861 (mp) REVERT: W 500 GLU cc_start: 0.8543 (tt0) cc_final: 0.8318 (mt-10) REVERT: E 5 LYS cc_start: 0.9136 (mtpm) cc_final: 0.8836 (tttp) REVERT: E 103 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: G 3 MET cc_start: 0.7691 (tpp) cc_final: 0.7287 (tpp) REVERT: G 14 GLU cc_start: 0.7353 (tp30) cc_final: 0.6947 (tp30) REVERT: G 37 ASN cc_start: 0.8273 (t0) cc_final: 0.8033 (t0) REVERT: G 103 GLN cc_start: 0.8941 (mm110) cc_final: 0.8636 (mp10) REVERT: H 13 ARG cc_start: 0.8712 (mmt90) cc_final: 0.8402 (mmm-85) REVERT: H 29 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8346 (mtp) REVERT: H 88 ASP cc_start: 0.9214 (m-30) cc_final: 0.8701 (t0) REVERT: H 117 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8135 (mt-10) REVERT: F 14 GLU cc_start: 0.8004 (tp30) cc_final: 0.7665 (tp30) REVERT: F 76 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7580 (mtpt) REVERT: F 109 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7989 (mmt) REVERT: J 500 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7965 (pt0) outliers start: 112 outliers final: 45 residues processed: 671 average time/residue: 0.6212 time to fit residues: 468.5750 Evaluate side-chains 643 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 585 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 483 ILE Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 204 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 68 GLN C 74 HIS C 103 GLN D 68 GLN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 72 ASN N 74 HIS M 18 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN T 110 GLN R 48 ASN R 68 GLN R 72 ASN R 101 ASN Q 68 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN E 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.120037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093140 restraints weight = 71939.871| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 5.37 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20223 Z= 0.201 Angle : 0.694 9.935 27351 Z= 0.349 Chirality : 0.047 0.244 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.127 57.959 2710 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.84 % Allowed : 30.37 % Favored : 63.79 % 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: 1.53 (0.18), residues: 2415 helix: 2.15 (0.20), residues: 636 sheet: 0.15 (0.19), residues: 738 loop : 1.18 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 63 TYR 0.023 0.002 TYR N 40 PHE 0.032 0.002 PHE H 15 TRP 0.007 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00470 (20223) covalent geometry : angle 0.69380 (27351) hydrogen bonds : bond 0.03807 ( 909) hydrogen bonds : angle 4.96854 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 598 time to evaluate : 0.855 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: A 5 LYS cc_start: 0.8718 (mtpm) cc_final: 0.8509 (mtpt) REVERT: A 32 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8306 (mtp180) REVERT: A 68 GLN cc_start: 0.8335 (mm110) cc_final: 0.8120 (mm-40) REVERT: A 88 ASP cc_start: 0.8285 (t0) cc_final: 0.7949 (t0) REVERT: A 134 GLN cc_start: 0.7512 (tt0) cc_final: 0.6867 (tt0) REVERT: C 14 GLU cc_start: 0.7264 (tp30) cc_final: 0.6858 (tp30) REVERT: C 63 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8522 (tmm-80) REVERT: C 88 ASP cc_start: 0.8488 (t0) cc_final: 0.8210 (t0) REVERT: C 103 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8536 (mm-40) REVERT: C 109 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: D 14 GLU cc_start: 0.9003 (tp30) cc_final: 0.8757 (tp30) REVERT: D 17 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8537 (tmm-80) REVERT: D 29 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7957 (mtp) REVERT: D 72 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8575 (t0) REVERT: D 93 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 14 GLU cc_start: 0.7805 (tp30) cc_final: 0.7462 (tp30) REVERT: B 50 LYS cc_start: 0.8817 (pttt) cc_final: 0.8583 (mmmt) REVERT: B 66 MET cc_start: 0.8725 (mmm) cc_final: 0.8401 (mmm) REVERT: P 5 LYS cc_start: 0.9226 (mtpm) cc_final: 0.8871 (tttp) REVERT: P 68 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: P 81 ASP cc_start: 0.7723 (m-30) cc_final: 0.7284 (t0) REVERT: P 87 ASN cc_start: 0.9298 (m-40) cc_final: 0.8982 (m-40) REVERT: P 103 GLN cc_start: 0.8697 (mm110) cc_final: 0.8413 (mt0) REVERT: N 14 GLU cc_start: 0.7109 (tp30) cc_final: 0.6665 (tp30) REVERT: N 103 GLN cc_start: 0.8902 (mm110) cc_final: 0.8386 (mp10) REVERT: M 14 GLU cc_start: 0.8971 (tp30) cc_final: 0.8729 (tp30) REVERT: M 17 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8624 (ttp80) REVERT: M 25 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: M 29 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7949 (mtt) REVERT: M 32 ARG cc_start: 0.8964 (mmm-85) cc_final: 0.8565 (mmm-85) REVERT: M 68 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: M 88 ASP cc_start: 0.9093 (m-30) cc_final: 0.8722 (t0) REVERT: O 14 GLU cc_start: 0.7770 (tp30) cc_final: 0.7492 (tp30) REVERT: O 50 LYS cc_start: 0.8721 (pptt) cc_final: 0.8149 (mmmt) REVERT: O 66 MET cc_start: 0.8659 (mmm) cc_final: 0.8448 (mmm) REVERT: O 95 MET cc_start: 0.8791 (mtm) cc_final: 0.8299 (mtp) REVERT: T 14 GLU cc_start: 0.8389 (tp30) cc_final: 0.7702 (tp30) REVERT: T 53 ASP cc_start: 0.8842 (p0) cc_final: 0.8625 (p0) REVERT: T 87 ASN cc_start: 0.9012 (m-40) cc_final: 0.8679 (m110) REVERT: T 88 ASP cc_start: 0.8475 (t0) cc_final: 0.8202 (t0) REVERT: R 14 GLU cc_start: 0.7145 (tp30) cc_final: 0.6727 (tp30) REVERT: R 25 GLN cc_start: 0.8534 (mm-40) cc_final: 0.7853 (mm110) REVERT: R 36 LYS cc_start: 0.8882 (mptt) cc_final: 0.8495 (mppt) REVERT: R 88 ASP cc_start: 0.8524 (t0) cc_final: 0.8262 (t0) REVERT: Q 14 GLU cc_start: 0.8964 (tp30) cc_final: 0.8697 (tp30) REVERT: Q 17 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8382 (ttp80) REVERT: Q 25 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: Q 29 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8199 (mtt) REVERT: Q 68 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7770 (tp40) REVERT: S 14 GLU cc_start: 0.7811 (tp30) cc_final: 0.7420 (tp30) REVERT: S 46 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6298 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8778 (pptt) cc_final: 0.8274 (pmtt) REVERT: S 66 MET cc_start: 0.8728 (mmm) cc_final: 0.8477 (mmm) REVERT: S 109 MET cc_start: 0.7768 (mmt) cc_final: 0.7187 (mmt) REVERT: X 504 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7891 (mp) REVERT: E 5 LYS cc_start: 0.9093 (mtpm) cc_final: 0.8774 (tttp) REVERT: E 76 LYS cc_start: 0.8482 (tppp) cc_final: 0.8219 (tptt) REVERT: E 103 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7764 (mt0) REVERT: G 3 MET cc_start: 0.7603 (tpp) cc_final: 0.7214 (tpp) REVERT: G 14 GLU cc_start: 0.7113 (tp30) cc_final: 0.6707 (tp30) REVERT: G 37 ASN cc_start: 0.8343 (t0) cc_final: 0.8098 (t0) REVERT: G 103 GLN cc_start: 0.8849 (mm110) cc_final: 0.8422 (mp10) REVERT: H 13 ARG cc_start: 0.8623 (mmt90) cc_final: 0.8131 (mmm-85) REVERT: H 29 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: H 88 ASP cc_start: 0.9085 (m-30) cc_final: 0.8568 (t0) REVERT: H 117 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8163 (mt-10) REVERT: F 14 GLU cc_start: 0.7631 (tp30) cc_final: 0.7309 (tp30) REVERT: F 76 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7527 (mtpt) REVERT: J 500 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8024 (pt0) outliers start: 126 outliers final: 69 residues processed: 652 average time/residue: 0.6513 time to fit residues: 475.8278 Evaluate side-chains 651 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 567 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 105 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 504 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 474 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 487 SER Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 37 ASN C 68 GLN D 68 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 134 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN N 24 ASN N 68 GLN N 72 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN T 110 GLN R 37 ASN R 68 GLN R 72 ASN R 74 HIS R 101 ASN Q 68 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.123891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098883 restraints weight = 44128.625| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.36 r_work: 0.3364 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20223 Z= 0.140 Angle : 0.688 10.891 27351 Z= 0.343 Chirality : 0.046 0.229 2905 Planarity : 0.004 0.048 3638 Dihedral : 4.909 56.357 2710 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.15 % Allowed : 32.08 % Favored : 62.77 % 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: 1.59 (0.19), residues: 2415 helix: 2.21 (0.20), residues: 636 sheet: 0.20 (0.19), residues: 738 loop : 1.21 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.022 0.001 TYR N 40 PHE 0.024 0.002 PHE I 475 TRP 0.006 0.001 TRP I 509 HIS 0.004 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00325 (20223) covalent geometry : angle 0.68834 (27351) hydrogen bonds : bond 0.03467 ( 909) hydrogen bonds : angle 4.86153 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 619 time to evaluate : 0.788 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: A 14 GLU cc_start: 0.8478 (tp30) cc_final: 0.7850 (tp30) REVERT: A 68 GLN cc_start: 0.8404 (mm110) cc_final: 0.8198 (mm-40) REVERT: A 87 ASN cc_start: 0.9102 (m-40) cc_final: 0.8765 (m-40) REVERT: A 88 ASP cc_start: 0.8342 (t0) cc_final: 0.7997 (t0) REVERT: A 110 GLN cc_start: 0.9206 (tt0) cc_final: 0.9002 (tt0) REVERT: A 134 GLN cc_start: 0.7610 (tt0) cc_final: 0.7353 (tp40) REVERT: C 14 GLU cc_start: 0.7486 (tp30) cc_final: 0.7091 (tp30) REVERT: C 63 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8508 (tmm-80) REVERT: C 88 ASP cc_start: 0.8360 (t0) cc_final: 0.8044 (t0) REVERT: C 101 ASN cc_start: 0.8970 (m-40) cc_final: 0.8557 (m110) REVERT: C 103 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8647 (mm-40) REVERT: C 109 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8319 (mtp) REVERT: D 13 ARG cc_start: 0.8866 (mmt90) cc_final: 0.8458 (mmm-85) REVERT: D 14 GLU cc_start: 0.9070 (tp30) cc_final: 0.8747 (tp30) REVERT: D 17 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8586 (ttp80) REVERT: D 29 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8349 (mtp) REVERT: D 93 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7805 (tm-30) REVERT: D 134 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: B 14 GLU cc_start: 0.8130 (tp30) cc_final: 0.7865 (tp30) REVERT: B 50 LYS cc_start: 0.8874 (pttt) cc_final: 0.8616 (mmmt) REVERT: B 66 MET cc_start: 0.8807 (mmm) cc_final: 0.8453 (mmm) REVERT: I 500 GLU cc_start: 0.8042 (tt0) cc_final: 0.7837 (tt0) REVERT: I 504 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8727 (mp) REVERT: P 5 LYS cc_start: 0.9223 (mtpm) cc_final: 0.8881 (tttp) REVERT: P 68 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: P 78 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8776 (mmm160) REVERT: P 81 ASP cc_start: 0.7986 (m-30) cc_final: 0.7483 (t0) REVERT: P 87 ASN cc_start: 0.9321 (m-40) cc_final: 0.9003 (m-40) REVERT: P 103 GLN cc_start: 0.8866 (mm110) cc_final: 0.8609 (mt0) REVERT: N 14 GLU cc_start: 0.7319 (tp30) cc_final: 0.6888 (tp30) REVERT: N 36 LYS cc_start: 0.8822 (tptp) cc_final: 0.8352 (mppt) REVERT: N 63 ARG cc_start: 0.8991 (mtp85) cc_final: 0.8750 (ttm-80) REVERT: N 68 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: N 88 ASP cc_start: 0.8304 (t0) cc_final: 0.8020 (t0) REVERT: N 103 GLN cc_start: 0.8967 (mm110) cc_final: 0.8556 (mp10) REVERT: M 14 GLU cc_start: 0.9016 (tp30) cc_final: 0.8795 (tp30) REVERT: M 32 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8629 (mmm-85) REVERT: M 68 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: M 88 ASP cc_start: 0.9173 (m-30) cc_final: 0.8781 (t0) REVERT: O 14 GLU cc_start: 0.8161 (tp30) cc_final: 0.7876 (tp30) REVERT: O 66 MET cc_start: 0.8753 (mmm) cc_final: 0.8379 (mmm) REVERT: O 117 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8386 (mm-30) REVERT: T 5 LYS cc_start: 0.8992 (mtpm) cc_final: 0.8678 (ttmt) REVERT: T 14 GLU cc_start: 0.8650 (tp30) cc_final: 0.8070 (tp30) REVERT: T 87 ASN cc_start: 0.9087 (m-40) cc_final: 0.8758 (m-40) REVERT: T 88 ASP cc_start: 0.8516 (t0) cc_final: 0.8180 (t0) REVERT: R 14 GLU cc_start: 0.7398 (tp30) cc_final: 0.6985 (tp30) REVERT: R 25 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8021 (mm110) REVERT: R 36 LYS cc_start: 0.8929 (mptt) cc_final: 0.8503 (mppt) REVERT: R 88 ASP cc_start: 0.8397 (t0) cc_final: 0.8070 (t0) REVERT: Q 14 GLU cc_start: 0.9031 (tp30) cc_final: 0.8736 (tp30) REVERT: Q 17 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8585 (ttp80) REVERT: Q 29 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8544 (mtt) REVERT: Q 68 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7965 (tp40) REVERT: Q 71 THR cc_start: 0.8774 (t) cc_final: 0.8160 (p) REVERT: S 14 GLU cc_start: 0.8185 (tp30) cc_final: 0.7755 (tp30) REVERT: S 46 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.6485 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8862 (pptt) cc_final: 0.8340 (pmtt) REVERT: S 66 MET cc_start: 0.8808 (mmm) cc_final: 0.8526 (mmm) REVERT: S 109 MET cc_start: 0.8317 (mmt) cc_final: 0.7886 (mmt) REVERT: S 110 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: X 504 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (mp) REVERT: W 500 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8140 (mt-10) REVERT: E 5 LYS cc_start: 0.9130 (mtpm) cc_final: 0.8811 (tttp) REVERT: E 76 LYS cc_start: 0.8572 (tppp) cc_final: 0.7831 (tptt) REVERT: G 3 MET cc_start: 0.7669 (tpp) cc_final: 0.7273 (tpp) REVERT: G 14 GLU cc_start: 0.7344 (tp30) cc_final: 0.6939 (tp30) REVERT: G 37 ASN cc_start: 0.8365 (t0) cc_final: 0.8092 (t0) REVERT: G 88 ASP cc_start: 0.8278 (t0) cc_final: 0.7951 (t0) REVERT: G 103 GLN cc_start: 0.8920 (mm110) cc_final: 0.8437 (mp10) REVERT: H 13 ARG cc_start: 0.8727 (mmt90) cc_final: 0.8420 (mmm-85) REVERT: H 14 GLU cc_start: 0.9036 (tp30) cc_final: 0.8706 (tp30) REVERT: H 29 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8379 (mtp) REVERT: H 88 ASP cc_start: 0.9205 (m-30) cc_final: 0.8658 (t0) REVERT: H 117 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8127 (mt-10) REVERT: F 14 GLU cc_start: 0.8089 (tp30) cc_final: 0.7763 (tp30) REVERT: F 76 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7584 (mtpt) REVERT: F 109 MET cc_start: 0.8143 (mmt) cc_final: 0.7892 (mmt) REVERT: F 123 LYS cc_start: 0.8865 (tppt) cc_final: 0.8650 (tppt) REVERT: J 484 GLU cc_start: 0.8558 (mp0) cc_final: 0.8349 (mp0) REVERT: J 500 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8027 (pt0) outliers start: 111 outliers final: 58 residues processed: 672 average time/residue: 0.6385 time to fit residues: 482.7410 Evaluate side-chains 664 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 592 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain L residue 483 ILE Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 54 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 68 GLN C 74 HIS D 68 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN ** P 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN N 74 HIS M 18 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN T 110 GLN R 68 GLN R 72 ASN R 101 ASN Q 68 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.121675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096006 restraints weight = 58791.540| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 4.91 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20223 Z= 0.174 Angle : 0.712 11.124 27351 Z= 0.355 Chirality : 0.047 0.234 2905 Planarity : 0.004 0.083 3638 Dihedral : 4.838 57.802 2705 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.70 % Allowed : 32.17 % Favored : 62.12 % 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: 1.58 (0.19), residues: 2415 helix: 2.19 (0.20), residues: 636 sheet: 0.20 (0.19), residues: 738 loop : 1.20 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 63 TYR 0.023 0.002 TYR N 40 PHE 0.027 0.002 PHE M 15 TRP 0.007 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00408 (20223) covalent geometry : angle 0.71152 (27351) hydrogen bonds : bond 0.03643 ( 909) hydrogen bonds : angle 4.92060 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 593 time to evaluate : 0.801 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: A 14 GLU cc_start: 0.8313 (tp30) cc_final: 0.7619 (tp30) REVERT: A 87 ASN cc_start: 0.8997 (m-40) cc_final: 0.8665 (m-40) REVERT: A 88 ASP cc_start: 0.8293 (t0) cc_final: 0.7979 (t0) REVERT: A 103 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7310 (mt0) REVERT: C 14 GLU cc_start: 0.7273 (tp30) cc_final: 0.6853 (tp30) REVERT: C 63 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8489 (tmm-80) REVERT: C 88 ASP cc_start: 0.8437 (t0) cc_final: 0.8127 (t0) REVERT: C 103 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8625 (mm-40) REVERT: C 109 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: D 13 ARG cc_start: 0.8731 (mmt90) cc_final: 0.8298 (mmm-85) REVERT: D 14 GLU cc_start: 0.9029 (tp30) cc_final: 0.8621 (tp30) REVERT: D 17 ARG cc_start: 0.8772 (ttp80) cc_final: 0.8449 (ttp80) REVERT: D 29 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7930 (mtp) REVERT: D 93 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7806 (tm-30) REVERT: D 134 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 14 GLU cc_start: 0.7779 (tp30) cc_final: 0.7488 (tp30) REVERT: B 50 LYS cc_start: 0.8831 (pttt) cc_final: 0.8596 (mmmt) REVERT: B 66 MET cc_start: 0.8768 (mmm) cc_final: 0.8396 (mmm) REVERT: I 504 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8782 (mp) REVERT: P 5 LYS cc_start: 0.9210 (mtpm) cc_final: 0.8881 (tttp) REVERT: P 68 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7185 (mt0) REVERT: P 81 ASP cc_start: 0.7621 (m-30) cc_final: 0.7275 (t0) REVERT: P 87 ASN cc_start: 0.9287 (m-40) cc_final: 0.8951 (m-40) REVERT: P 103 GLN cc_start: 0.8690 (mm110) cc_final: 0.8445 (mt0) REVERT: P 136 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8481 (mt-10) REVERT: N 14 GLU cc_start: 0.7099 (tp30) cc_final: 0.6645 (tp30) REVERT: N 68 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: N 88 ASP cc_start: 0.8344 (t0) cc_final: 0.8044 (t0) REVERT: N 103 GLN cc_start: 0.8947 (mm110) cc_final: 0.8523 (mp10) REVERT: N 109 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8695 (mtt) REVERT: M 14 GLU cc_start: 0.8978 (tp30) cc_final: 0.8599 (tp30) REVERT: M 17 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8567 (tmm-80) REVERT: M 32 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8447 (mmm-85) REVERT: M 68 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: M 88 ASP cc_start: 0.9060 (m-30) cc_final: 0.8685 (t0) REVERT: O 50 LYS cc_start: 0.8653 (pptt) cc_final: 0.8244 (mmtt) REVERT: O 66 MET cc_start: 0.8687 (mmm) cc_final: 0.8397 (mmm) REVERT: O 117 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8437 (mm-30) REVERT: T 5 LYS cc_start: 0.8992 (mtpm) cc_final: 0.8685 (ttmt) REVERT: T 14 GLU cc_start: 0.8409 (tp30) cc_final: 0.7768 (tp30) REVERT: T 60 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8239 (mp0) REVERT: T 87 ASN cc_start: 0.8995 (m-40) cc_final: 0.8689 (m-40) REVERT: T 88 ASP cc_start: 0.8451 (t0) cc_final: 0.8086 (t0) REVERT: R 14 GLU cc_start: 0.7129 (tp30) cc_final: 0.6713 (tp30) REVERT: R 25 GLN cc_start: 0.8551 (mm-40) cc_final: 0.7865 (mm110) REVERT: R 36 LYS cc_start: 0.8919 (mptt) cc_final: 0.8523 (mppt) REVERT: R 74 HIS cc_start: 0.7524 (m90) cc_final: 0.7286 (m90) REVERT: R 88 ASP cc_start: 0.8445 (t0) cc_final: 0.8145 (t0) REVERT: Q 29 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: Q 68 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7671 (tp40) REVERT: S 14 GLU cc_start: 0.7814 (tp30) cc_final: 0.7411 (tp30) REVERT: S 46 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6340 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8795 (pptt) cc_final: 0.8277 (pmtt) REVERT: S 66 MET cc_start: 0.8755 (mmm) cc_final: 0.8455 (mmm) REVERT: S 109 MET cc_start: 0.7605 (mmt) cc_final: 0.7080 (mmt) REVERT: S 110 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: X 504 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7868 (mp) REVERT: W 500 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8181 (mt-10) REVERT: E 5 LYS cc_start: 0.9105 (mtpm) cc_final: 0.8788 (tttp) REVERT: E 68 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7863 (mm-40) REVERT: E 76 LYS cc_start: 0.8473 (tppp) cc_final: 0.7993 (tptt) REVERT: G 3 MET cc_start: 0.7524 (tpp) cc_final: 0.7150 (tpp) REVERT: G 14 GLU cc_start: 0.7092 (tp30) cc_final: 0.6661 (tp30) REVERT: G 37 ASN cc_start: 0.8395 (t0) cc_final: 0.8134 (t0) REVERT: G 88 ASP cc_start: 0.8267 (t0) cc_final: 0.8036 (t0) REVERT: G 103 GLN cc_start: 0.8863 (mm110) cc_final: 0.8360 (mp10) REVERT: H 13 ARG cc_start: 0.8636 (mmt90) cc_final: 0.8291 (mmm-85) REVERT: H 29 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7971 (mtp) REVERT: H 88 ASP cc_start: 0.9070 (m-30) cc_final: 0.8532 (t0) REVERT: H 109 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7463 (ttt) REVERT: H 117 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8193 (mt-10) REVERT: F 14 GLU cc_start: 0.7674 (tp30) cc_final: 0.7426 (tp30) REVERT: F 76 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7504 (mtpt) REVERT: F 109 MET cc_start: 0.7775 (mmt) cc_final: 0.7294 (mmt) REVERT: J 500 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: J 502 ASP cc_start: 0.8411 (m-30) cc_final: 0.8089 (m-30) outliers start: 123 outliers final: 65 residues processed: 643 average time/residue: 0.6579 time to fit residues: 474.5813 Evaluate side-chains 664 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 582 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 504 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 HIS Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 37 ASN C 68 GLN D 68 GLN D 72 ASN D 134 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 58 GLN N 68 GLN N 72 ASN M 18 GLN ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 110 GLN R 37 ASN R 68 GLN R 72 ASN R 101 ASN Q 68 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096995 restraints weight = 48590.304| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.53 r_work: 0.3312 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20223 Z= 0.171 Angle : 0.731 12.602 27351 Z= 0.364 Chirality : 0.047 0.237 2905 Planarity : 0.004 0.049 3638 Dihedral : 4.838 58.018 2705 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.96 % Allowed : 33.70 % Favored : 61.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.55 (0.19), residues: 2415 helix: 2.14 (0.20), residues: 636 sheet: 0.21 (0.19), residues: 738 loop : 1.17 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 63 TYR 0.022 0.001 TYR N 40 PHE 0.028 0.002 PHE I 475 TRP 0.007 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00404 (20223) covalent geometry : angle 0.73098 (27351) hydrogen bonds : bond 0.03662 ( 909) hydrogen bonds : angle 4.96837 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 592 time to evaluate : 0.844 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: A 14 GLU cc_start: 0.8505 (tp30) cc_final: 0.7874 (tp30) REVERT: A 87 ASN cc_start: 0.9090 (m-40) cc_final: 0.8746 (m-40) REVERT: A 88 ASP cc_start: 0.8419 (t0) cc_final: 0.8103 (t0) REVERT: C 14 GLU cc_start: 0.7512 (tp30) cc_final: 0.7112 (tp30) REVERT: C 63 ARG cc_start: 0.8835 (ttp80) cc_final: 0.8527 (tmm-80) REVERT: C 88 ASP cc_start: 0.8428 (t0) cc_final: 0.8092 (t0) REVERT: C 101 ASN cc_start: 0.8939 (m-40) cc_final: 0.8628 (m110) REVERT: C 103 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8674 (mm-40) REVERT: C 109 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8381 (mtp) REVERT: D 13 ARG cc_start: 0.8882 (mmt90) cc_final: 0.8470 (mmm-85) REVERT: D 14 GLU cc_start: 0.9092 (tp30) cc_final: 0.8734 (tp30) REVERT: D 17 ARG cc_start: 0.8900 (ttp80) cc_final: 0.8608 (ttp80) REVERT: D 29 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8280 (mtp) REVERT: D 93 GLN cc_start: 0.8398 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 134 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: B 14 GLU cc_start: 0.8139 (tp30) cc_final: 0.7855 (tp30) REVERT: B 50 LYS cc_start: 0.8846 (pttt) cc_final: 0.8601 (mmmt) REVERT: B 66 MET cc_start: 0.8833 (mmm) cc_final: 0.8471 (mmm) REVERT: I 475 PHE cc_start: 0.7087 (m-10) cc_final: 0.6659 (m-10) REVERT: I 504 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8767 (mp) REVERT: P 5 LYS cc_start: 0.9210 (mtpm) cc_final: 0.8883 (tttp) REVERT: P 68 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: P 81 ASP cc_start: 0.8004 (m-30) cc_final: 0.7483 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9321 (m-40) cc_final: 0.8985 (m-40) REVERT: P 103 GLN cc_start: 0.8888 (mm110) cc_final: 0.8671 (mt0) REVERT: P 109 MET cc_start: 0.8696 (ptm) cc_final: 0.8408 (ptm) REVERT: P 136 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8701 (mt-10) REVERT: N 14 GLU cc_start: 0.7358 (tp30) cc_final: 0.6932 (tp30) REVERT: N 36 LYS cc_start: 0.8803 (tptp) cc_final: 0.8343 (mppt) REVERT: N 68 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: N 74 HIS cc_start: 0.7774 (m90) cc_final: 0.7555 (m-70) REVERT: N 88 ASP cc_start: 0.8372 (t0) cc_final: 0.8069 (t0) REVERT: N 103 GLN cc_start: 0.9019 (mm110) cc_final: 0.8597 (mp10) REVERT: M 14 GLU cc_start: 0.9048 (tp30) cc_final: 0.8761 (tp30) REVERT: M 32 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8650 (mmm-85) REVERT: M 68 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: M 88 ASP cc_start: 0.9182 (m-30) cc_final: 0.8798 (t0) REVERT: O 50 LYS cc_start: 0.8678 (pptt) cc_final: 0.8271 (mmtt) REVERT: O 66 MET cc_start: 0.8780 (mmm) cc_final: 0.8500 (mmm) REVERT: O 117 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8325 (mm-30) REVERT: U 500 GLU cc_start: 0.8532 (tt0) cc_final: 0.8066 (tt0) REVERT: T 5 LYS cc_start: 0.8981 (mtpm) cc_final: 0.8674 (ttmt) REVERT: T 14 GLU cc_start: 0.8651 (tp30) cc_final: 0.8072 (tp30) REVERT: T 60 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8394 (mp0) REVERT: T 76 LYS cc_start: 0.8547 (tptm) cc_final: 0.8279 (tptp) REVERT: T 87 ASN cc_start: 0.9082 (m-40) cc_final: 0.8777 (m-40) REVERT: T 88 ASP cc_start: 0.8608 (t0) cc_final: 0.8283 (t0) REVERT: R 1 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6401 (ptm) REVERT: R 14 GLU cc_start: 0.7394 (tp30) cc_final: 0.6991 (tp30) REVERT: R 25 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8057 (mm110) REVERT: R 36 LYS cc_start: 0.8957 (mptt) cc_final: 0.8537 (mppt) REVERT: R 74 HIS cc_start: 0.7544 (m90) cc_final: 0.7305 (m90) REVERT: R 88 ASP cc_start: 0.8425 (t0) cc_final: 0.8093 (t0) REVERT: R 107 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7626 (mtp85) REVERT: Q 14 GLU cc_start: 0.9019 (tp30) cc_final: 0.8779 (tp30) REVERT: Q 29 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8435 (mtp) REVERT: Q 68 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7780 (tp40) REVERT: Q 71 THR cc_start: 0.8803 (t) cc_final: 0.8191 (p) REVERT: S 14 GLU cc_start: 0.8210 (tp30) cc_final: 0.7778 (tp30) REVERT: S 46 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6426 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8825 (pptt) cc_final: 0.8303 (pmtt) REVERT: S 66 MET cc_start: 0.8818 (mmm) cc_final: 0.8532 (mmm) REVERT: S 109 MET cc_start: 0.8231 (mmt) cc_final: 0.7756 (mmt) REVERT: S 110 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: X 504 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7935 (mp) REVERT: W 500 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8168 (mt-10) REVERT: E 5 LYS cc_start: 0.9152 (mtpm) cc_final: 0.8823 (tttp) REVERT: E 68 GLN cc_start: 0.8264 (mm-40) cc_final: 0.8045 (mm-40) REVERT: E 76 LYS cc_start: 0.8602 (tppp) cc_final: 0.8326 (tptt) REVERT: G 3 MET cc_start: 0.7709 (tpp) cc_final: 0.7307 (tpp) REVERT: G 14 GLU cc_start: 0.7378 (tp30) cc_final: 0.6954 (tp30) REVERT: G 37 ASN cc_start: 0.8457 (t0) cc_final: 0.8211 (t0) REVERT: G 88 ASP cc_start: 0.8289 (t0) cc_final: 0.8023 (t0) REVERT: G 103 GLN cc_start: 0.8926 (mm110) cc_final: 0.8341 (mp10) REVERT: H 13 ARG cc_start: 0.8766 (mmt90) cc_final: 0.8427 (mmm-85) REVERT: H 29 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8365 (mtp) REVERT: H 71 THR cc_start: 0.9045 (t) cc_final: 0.8270 (p) REVERT: H 88 ASP cc_start: 0.9198 (m-30) cc_final: 0.8658 (t0) REVERT: H 95 MET cc_start: 0.7753 (mtt) cc_final: 0.7328 (mtt) REVERT: H 109 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7024 (tpt) REVERT: H 117 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8153 (mt-10) REVERT: F 14 GLU cc_start: 0.8119 (tp30) cc_final: 0.7875 (tp30) REVERT: F 76 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7572 (mtpt) REVERT: J 500 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8071 (pt0) outliers start: 107 outliers final: 68 residues processed: 638 average time/residue: 0.6582 time to fit residues: 471.4272 Evaluate side-chains 659 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 504 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 HIS Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 227 optimal weight: 0.0040 chunk 115 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 103 GLN C 24 ASN C 68 GLN C 74 HIS D 68 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN ** P 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN N 68 GLN M 18 GLN ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 GLN R 68 GLN R 72 ASN R 101 ASN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS G 101 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.123015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.096873 restraints weight = 61025.809| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 5.03 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20223 Z= 0.163 Angle : 0.744 12.269 27351 Z= 0.371 Chirality : 0.047 0.237 2905 Planarity : 0.004 0.052 3638 Dihedral : 4.829 57.466 2705 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.40 % Allowed : 34.45 % Favored : 61.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.52 (0.18), residues: 2415 helix: 2.19 (0.20), residues: 628 sheet: 0.20 (0.19), residues: 738 loop : 1.10 (0.23), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 32 TYR 0.023 0.001 TYR N 40 PHE 0.028 0.002 PHE I 475 TRP 0.006 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00385 (20223) covalent geometry : angle 0.74388 (27351) hydrogen bonds : bond 0.03646 ( 909) hydrogen bonds : angle 4.97197 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 594 time to evaluate : 0.789 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: A 14 GLU cc_start: 0.8309 (tp30) cc_final: 0.7610 (tp30) REVERT: A 87 ASN cc_start: 0.8996 (m-40) cc_final: 0.8666 (m-40) REVERT: A 88 ASP cc_start: 0.8329 (t0) cc_final: 0.8008 (t0) REVERT: C 14 GLU cc_start: 0.7234 (tp30) cc_final: 0.6820 (tp30) REVERT: C 63 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8516 (tmm-80) REVERT: C 88 ASP cc_start: 0.8409 (t0) cc_final: 0.8074 (t0) REVERT: C 101 ASN cc_start: 0.8904 (m-40) cc_final: 0.8575 (m110) REVERT: C 103 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8641 (mm-40) REVERT: C 109 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: D 13 ARG cc_start: 0.8760 (mmt90) cc_final: 0.8326 (mmm-85) REVERT: D 14 GLU cc_start: 0.9027 (tp30) cc_final: 0.8602 (tp30) REVERT: D 17 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8461 (ttp80) REVERT: D 29 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7927 (mtt) REVERT: D 93 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7963 (tm-30) REVERT: D 134 GLN cc_start: 0.7681 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 14 GLU cc_start: 0.7776 (tp30) cc_final: 0.7477 (tp30) REVERT: B 50 LYS cc_start: 0.8805 (pttt) cc_final: 0.8577 (mmmt) REVERT: B 66 MET cc_start: 0.8754 (mmm) cc_final: 0.8380 (mmm) REVERT: I 504 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8813 (mp) REVERT: P 5 LYS cc_start: 0.9212 (mtpm) cc_final: 0.8886 (tttp) REVERT: P 68 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: P 81 ASP cc_start: 0.7575 (m-30) cc_final: 0.7262 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9272 (m-40) cc_final: 0.8939 (m-40) REVERT: P 103 GLN cc_start: 0.8681 (mm110) cc_final: 0.8439 (mt0) REVERT: P 109 MET cc_start: 0.8557 (ptm) cc_final: 0.8188 (ptm) REVERT: P 136 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8459 (mt-10) REVERT: N 14 GLU cc_start: 0.7035 (tp30) cc_final: 0.6584 (tp30) REVERT: N 36 LYS cc_start: 0.8719 (tptp) cc_final: 0.8311 (mppt) REVERT: N 68 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7379 (mp10) REVERT: N 74 HIS cc_start: 0.7842 (m90) cc_final: 0.7609 (m-70) REVERT: N 88 ASP cc_start: 0.8337 (t0) cc_final: 0.8031 (t0) REVERT: N 103 GLN cc_start: 0.8959 (mm110) cc_final: 0.8572 (mp10) REVERT: M 17 ARG cc_start: 0.8718 (tmm-80) cc_final: 0.8447 (tmm-80) REVERT: M 32 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8409 (mmm-85) REVERT: M 68 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: M 88 ASP cc_start: 0.9021 (m-30) cc_final: 0.8647 (t0) REVERT: O 50 LYS cc_start: 0.8652 (pptt) cc_final: 0.8232 (mmtt) REVERT: O 66 MET cc_start: 0.8693 (mmm) cc_final: 0.8406 (mmm) REVERT: O 117 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8441 (mm-30) REVERT: U 500 GLU cc_start: 0.8633 (tt0) cc_final: 0.8199 (tt0) REVERT: T 5 LYS cc_start: 0.8985 (mtpm) cc_final: 0.8669 (ttmt) REVERT: T 14 GLU cc_start: 0.8411 (tp30) cc_final: 0.7770 (tp30) REVERT: T 76 LYS cc_start: 0.8416 (tptm) cc_final: 0.8089 (tptp) REVERT: T 87 ASN cc_start: 0.9002 (m-40) cc_final: 0.8700 (m-40) REVERT: T 88 ASP cc_start: 0.8527 (t0) cc_final: 0.8199 (t0) REVERT: R 1 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6341 (ptm) REVERT: R 14 GLU cc_start: 0.7105 (tp30) cc_final: 0.6698 (tp30) REVERT: R 25 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7869 (mm110) REVERT: R 36 LYS cc_start: 0.8926 (mptt) cc_final: 0.8527 (mppt) REVERT: R 74 HIS cc_start: 0.7580 (m90) cc_final: 0.7329 (m90) REVERT: R 88 ASP cc_start: 0.8421 (t0) cc_final: 0.8099 (t0) REVERT: R 107 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7303 (mtp85) REVERT: Q 13 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: Q 29 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7823 (mtp) REVERT: Q 68 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7609 (tp40) REVERT: Q 71 THR cc_start: 0.8714 (t) cc_final: 0.8097 (p) REVERT: S 14 GLU cc_start: 0.7859 (tp30) cc_final: 0.7388 (tp30) REVERT: S 46 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6291 (p0) REVERT: S 50 LYS cc_start: 0.8789 (pptt) cc_final: 0.8271 (pmtt) REVERT: S 66 MET cc_start: 0.8764 (mmm) cc_final: 0.8469 (mmm) REVERT: S 109 MET cc_start: 0.7650 (mmt) cc_final: 0.7142 (mmt) REVERT: S 110 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: X 504 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7835 (mp) REVERT: W 500 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8230 (mt-10) REVERT: E 5 LYS cc_start: 0.9117 (mtpm) cc_final: 0.8797 (tttp) REVERT: E 68 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7846 (mm-40) REVERT: E 76 LYS cc_start: 0.8460 (tppp) cc_final: 0.8179 (tptt) REVERT: G 3 MET cc_start: 0.7477 (tpp) cc_final: 0.7106 (tpp) REVERT: G 14 GLU cc_start: 0.7047 (tp30) cc_final: 0.6614 (tp30) REVERT: G 37 ASN cc_start: 0.8418 (t0) cc_final: 0.8162 (t0) REVERT: G 88 ASP cc_start: 0.8265 (t0) cc_final: 0.7915 (t0) REVERT: G 101 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8890 (t0) REVERT: G 103 GLN cc_start: 0.8862 (mm110) cc_final: 0.8348 (mp10) REVERT: H 13 ARG cc_start: 0.8635 (mmt90) cc_final: 0.8278 (mmm-85) REVERT: H 29 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: H 71 THR cc_start: 0.8939 (t) cc_final: 0.8134 (p) REVERT: H 88 ASP cc_start: 0.9033 (m-30) cc_final: 0.8481 (t0) REVERT: H 109 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.6707 (tpt) REVERT: H 117 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8177 (mt-10) REVERT: F 14 GLU cc_start: 0.7705 (tp30) cc_final: 0.7439 (tp30) REVERT: F 76 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7512 (mtpt) REVERT: J 500 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8102 (pt0) outliers start: 95 outliers final: 62 residues processed: 637 average time/residue: 0.6572 time to fit residues: 469.9784 Evaluate side-chains 656 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 577 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 68 GLN Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain M residue 28 ASP Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 68 GLN Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 504 LEU Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 29 MET Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 74 HIS Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 135 optimal weight: 0.3980 chunk 188 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 24 ASN C 37 ASN C 68 GLN C 74 HIS D 68 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 68 GLN N 72 ASN M 18 GLN ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN T 110 GLN R 37 ASN R 68 GLN R 72 ASN R 101 ASN Q 68 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.123515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097756 restraints weight = 53537.243| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.75 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20223 Z= 0.159 Angle : 0.749 14.630 27351 Z= 0.371 Chirality : 0.047 0.235 2905 Planarity : 0.004 0.078 3638 Dihedral : 4.813 58.269 2705 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.36 % Allowed : 34.72 % Favored : 60.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.52 (0.19), residues: 2415 helix: 2.13 (0.20), residues: 636 sheet: 0.19 (0.19), residues: 738 loop : 1.14 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 63 TYR 0.022 0.001 TYR N 40 PHE 0.020 0.002 PHE H 15 TRP 0.006 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00374 (20223) covalent geometry : angle 0.74922 (27351) hydrogen bonds : bond 0.03613 ( 909) hydrogen bonds : angle 4.99258 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9107.32 seconds wall clock time: 155 minutes 57.51 seconds (9357.51 seconds total)