Starting phenix.real_space_refine on Tue May 20 05:12:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivr_60933/05_2025/9ivr_60933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivr_60933/05_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_60933/05_2025/9ivr_60933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivr_60933/05_2025/9ivr_60933.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivr_60933/05_2025/9ivr_60933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivr_60933/05_2025/9ivr_60933.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.26, per 1000 atoms: 0.62 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: 4.99 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.09 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: 6.21 Time building geometry restraints manager: 5.77 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.210 Process input model: 45.380 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 59.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP W 509 HIS 0.006 0.001 HIS C 79 PHE 0.020 0.002 PHE D 112 TYR 0.023 0.001 TYR N 40 ARG 0.009 0.001 ARG Q 32 Details of bonding type rmsd hydrogen bonds : bond 0.11616 ( 909) hydrogen bonds : angle 6.13908 ( 2565) covalent geometry : bond 0.00512 (20223) covalent geometry : angle 0.91868 (27351) *********************** 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 : 2.108 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: 0.8260 (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: N 14 GLU cc_start: 0.6999 (tp30) cc_final: 0.6698 (tp30) 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: 0.7258 (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: 0.7063 (mmt) outliers start: 33 outliers final: 22 residues processed: 671 average time/residue: 1.2880 time to fit residues: 971.2704 Evaluate side-chains 586 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 563 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain C residue 61 ILE 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 195 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 135 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 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 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** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 68 GLN T 68 GLN T 103 GLN T 110 GLN T 128 ASN R 72 ASN R 101 ASN S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN ** 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.124704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098899 restraints weight = 50968.038| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.69 r_work: 0.3345 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1663 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= 0.169 Angle : 0.657 10.432 27351 Z= 0.334 Chirality : 0.046 0.193 2905 Planarity : 0.004 0.059 3638 Dihedral : 5.710 67.171 2739 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.15 % Allowed : 27.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.19), residues: 2415 helix: 2.16 (0.20), residues: 636 sheet: 0.12 (0.18), residues: 742 loop : 1.17 (0.24), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 509 HIS 0.005 0.001 HIS C 62 PHE 0.026 0.002 PHE M 70 TYR 0.022 0.002 TYR N 40 ARG 0.008 0.001 ARG F 17 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 909) hydrogen bonds : angle 5.08209 ( 2565) covalent geometry : bond 0.00395 (20223) covalent geometry : angle 0.65706 (27351) *********************** 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 729 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 618 time to evaluate : 2.276 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: 0.8441 (mm110) cc_final: 0.8157 (mm-40) REVERT: A 103 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: C 14 GLU cc_start: 0.7544 (tp30) cc_final: 0.7206 (tp30) REVERT: C 63 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8705 (tmm-80) REVERT: C 103 GLN cc_start: 0.8944 (mm110) cc_final: 0.8568 (mm110) REVERT: D 13 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8469 (mmm-85) REVERT: D 32 ARG cc_start: 0.9086 (mmm-85) cc_final: 0.8854 (mmm-85) REVERT: D 81 ASP cc_start: 0.8126 (m-30) cc_final: 0.7814 (m-30) REVERT: B 14 GLU cc_start: 0.7910 (tp30) cc_final: 0.7678 (tp30) REVERT: B 46 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7120 (OUTLIER) REVERT: B 50 LYS cc_start: 0.8933 (pttt) cc_final: 0.8635 (pmtt) REVERT: B 53 ASP cc_start: 0.9110 (p0) cc_final: 0.8894 (p0) REVERT: I 500 GLU cc_start: 0.7966 (tt0) cc_final: 0.7735 (tt0) REVERT: P 29 MET cc_start: 0.8564 (mmp) cc_final: 0.8345 (mmm) REVERT: P 81 ASP cc_start: 0.8144 (m-30) cc_final: 0.7462 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9399 (m-40) cc_final: 0.9129 (m110) REVERT: P 88 ASP cc_start: 0.8777 (m-30) cc_final: 0.8162 (t0) REVERT: N 14 GLU cc_start: 0.7463 (tp30) cc_final: 0.7093 (tp30) REVERT: N 103 GLN cc_start: 0.8622 (mm110) cc_final: 0.8270 (mm110) REVERT: M 29 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8202 (mtt) REVERT: M 68 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8047 (pp30) REVERT: M 76 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8379 (mttt) REVERT: M 88 ASP cc_start: 0.9252 (m-30) cc_final: 0.8920 (t0) REVERT: O 14 GLU cc_start: 0.8215 (tp30) cc_final: 0.7870 (tp30) REVERT: O 50 LYS cc_start: 0.8464 (pptt) cc_final: 0.8177 (mmmt) REVERT: O 53 ASP cc_start: 0.9102 (p0) cc_final: 0.8875 (p0) REVERT: V 474 THR cc_start: 0.8485 (p) cc_final: 0.8097 (t) REVERT: U 500 GLU cc_start: 0.8510 (tt0) cc_final: 0.8231 (tt0) REVERT: T 14 GLU cc_start: 0.8560 (tp30) cc_final: 0.7972 (tp30) REVERT: T 53 ASP cc_start: 0.8809 (p0) cc_final: 0.8600 (p0) REVERT: T 76 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8102 (tptp) REVERT: R 14 GLU cc_start: 0.7437 (tp30) cc_final: 0.7106 (tp30) REVERT: R 36 LYS cc_start: 0.8739 (mptt) cc_final: 0.8380 (mppt) REVERT: R 72 ASN cc_start: 0.7392 (OUTLIER) cc_final: 0.7154 (p0) REVERT: R 103 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7853 (mm-40) REVERT: R 109 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: Q 14 GLU cc_start: 0.9069 (tp30) cc_final: 0.8846 (tp30) REVERT: Q 17 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8537 (ttp80) REVERT: Q 68 GLN cc_start: 0.8441 (tp40) cc_final: 0.7948 (tp40) REVERT: Q 69 ASN cc_start: 0.7457 (t0) cc_final: 0.7126 (t0) REVERT: S 14 GLU cc_start: 0.8032 (tp30) cc_final: 0.7698 (tp30) REVERT: S 46 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6879 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8824 (pptt) cc_final: 0.8418 (pmtt) REVERT: S 53 ASP cc_start: 0.9043 (p0) cc_final: 0.8807 (p0) REVERT: S 109 MET cc_start: 0.8159 (mmt) cc_final: 0.7837 (mmt) REVERT: X 504 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7967 (mp) REVERT: X 506 ASP cc_start: 0.7185 (t0) cc_final: 0.6867 (t0) REVERT: W 500 GLU cc_start: 0.8550 (tt0) cc_final: 0.8154 (mt-10) REVERT: E 5 LYS cc_start: 0.9193 (mtpm) cc_final: 0.8952 (tttp) REVERT: G 1 MET cc_start: 0.6340 (ttt) cc_final: 0.5980 (ttt) REVERT: G 3 MET cc_start: 0.7529 (tpp) cc_final: 0.7101 (tpp) REVERT: G 14 GLU cc_start: 0.7464 (tp30) cc_final: 0.7111 (tp30) REVERT: G 103 GLN cc_start: 0.8520 (mm110) cc_final: 0.8244 (mm110) REVERT: H 88 ASP cc_start: 0.9264 (m-30) cc_final: 0.8757 (t0) REVERT: F 14 GLU cc_start: 0.8079 (tp30) cc_final: 0.7864 (tp30) REVERT: F 53 ASP cc_start: 0.8994 (p0) cc_final: 0.8756 (p0) REVERT: J 500 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7749 (pt0) outliers start: 111 outliers final: 44 residues processed: 672 average time/residue: 1.3713 time to fit residues: 1039.0163 Evaluate side-chains 605 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 554 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR 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 46 ASP 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 U residue 505 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 41 VAL 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 R residue 109 MET 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 163 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 210 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN C 37 ASN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 GLN M 18 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 S 100 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 ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 122 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.121919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095478 restraints weight = 59175.743| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 5.00 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20223 Z= 0.198 Angle : 0.664 10.222 27351 Z= 0.336 Chirality : 0.046 0.190 2905 Planarity : 0.004 0.050 3638 Dihedral : 5.192 63.419 2708 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.61 % Allowed : 27.17 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 2415 helix: 2.21 (0.20), residues: 636 sheet: 0.14 (0.19), residues: 738 loop : 1.15 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 509 HIS 0.004 0.001 HIS A 79 PHE 0.021 0.002 PHE H 15 TYR 0.019 0.002 TYR G 20 ARG 0.015 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 909) hydrogen bonds : angle 4.99093 ( 2565) covalent geometry : bond 0.00462 (20223) covalent geometry : angle 0.66424 (27351) *********************** 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: 121 poor density : 604 time to evaluate : 2.100 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 5 LYS cc_start: 0.8724 (mtpm) cc_final: 0.8473 (mtpt) REVERT: A 88 ASP cc_start: 0.8005 (t0) cc_final: 0.7763 (t0) REVERT: A 103 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: C 14 GLU cc_start: 0.7340 (tp30) cc_final: 0.6942 (tp30) REVERT: C 103 GLN cc_start: 0.8917 (mm110) cc_final: 0.8462 (mm-40) REVERT: D 13 ARG cc_start: 0.8730 (mmt90) cc_final: 0.8339 (mmm-85) REVERT: D 14 GLU cc_start: 0.9027 (tp30) cc_final: 0.8801 (tp30) REVERT: D 17 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8536 (ttp80) REVERT: B 14 GLU cc_start: 0.7713 (tp30) cc_final: 0.7446 (tp30) REVERT: B 50 LYS cc_start: 0.8891 (pttt) cc_final: 0.8649 (mmmt) REVERT: B 53 ASP cc_start: 0.9018 (p0) cc_final: 0.8814 (p0) REVERT: B 109 MET cc_start: 0.8284 (mmt) cc_final: 0.8019 (mmt) REVERT: P 68 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: P 81 ASP cc_start: 0.7780 (m-30) cc_final: 0.7198 (t0) REVERT: P 87 ASN cc_start: 0.9368 (m-40) cc_final: 0.9127 (m-40) REVERT: P 103 GLN cc_start: 0.8706 (mm110) cc_final: 0.8446 (mt0) REVERT: P 132 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7625 (mmt-90) REVERT: N 14 GLU cc_start: 0.7166 (tp30) cc_final: 0.6725 (tp30) REVERT: N 60 GLU cc_start: 0.6696 (pp20) cc_final: 0.6470 (pp20) REVERT: N 103 GLN cc_start: 0.8676 (mm110) cc_final: 0.8209 (mp10) REVERT: M 29 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7973 (mtt) REVERT: M 68 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: M 76 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8304 (mttt) REVERT: M 88 ASP cc_start: 0.9085 (m-30) cc_final: 0.8739 (t0) REVERT: M 109 MET cc_start: 0.8017 (ptm) cc_final: 0.7754 (ttt) REVERT: O 14 GLU cc_start: 0.7803 (tp30) cc_final: 0.7556 (tp30) REVERT: O 50 LYS cc_start: 0.8707 (pptt) cc_final: 0.8455 (pmtt) REVERT: O 53 ASP cc_start: 0.9006 (p0) cc_final: 0.8800 (p0) REVERT: O 66 MET cc_start: 0.8484 (mmm) cc_final: 0.8226 (mmm) REVERT: O 95 MET cc_start: 0.8836 (mtm) cc_final: 0.8329 (mtp) REVERT: O 123 LYS cc_start: 0.8855 (tppp) cc_final: 0.8622 (tppp) REVERT: V 474 THR cc_start: 0.8533 (p) cc_final: 0.8079 (t) REVERT: T 14 GLU cc_start: 0.8377 (tp30) cc_final: 0.7707 (tp30) REVERT: T 76 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7917 (tptp) REVERT: T 88 ASP cc_start: 0.8375 (t0) cc_final: 0.8164 (t0) REVERT: R 14 GLU cc_start: 0.7269 (tp30) cc_final: 0.6871 (tp30) REVERT: R 25 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7889 (mm110) REVERT: R 36 LYS cc_start: 0.8787 (mptt) cc_final: 0.8416 (mppt) REVERT: R 103 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7906 (mp10) REVERT: Q 17 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8516 (ttp80) REVERT: Q 29 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: Q 68 GLN cc_start: 0.8280 (tp40) cc_final: 0.7910 (tp40) REVERT: Q 76 LYS cc_start: 0.8474 (mttt) cc_final: 0.8263 (mttm) REVERT: S 14 GLU cc_start: 0.7734 (tp30) cc_final: 0.7306 (tp30) REVERT: S 46 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6624 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8814 (pptt) cc_final: 0.8370 (pmtt) REVERT: S 53 ASP cc_start: 0.9024 (p0) cc_final: 0.8803 (p0) REVERT: S 66 MET cc_start: 0.8608 (mmm) cc_final: 0.8353 (mmm) REVERT: S 109 MET cc_start: 0.7755 (mmt) cc_final: 0.7178 (mmt) REVERT: S 110 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: X 504 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7971 (mp) REVERT: W 500 GLU cc_start: 0.8517 (tt0) cc_final: 0.8221 (mt-10) REVERT: E 5 LYS cc_start: 0.9144 (mtpm) cc_final: 0.8915 (tttp) REVERT: E 36 LYS cc_start: 0.9014 (tppp) cc_final: 0.8813 (tppp) REVERT: E 103 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: G 1 MET cc_start: 0.6373 (ttt) cc_final: 0.6166 (ttt) REVERT: G 3 MET cc_start: 0.7496 (tpp) cc_final: 0.7103 (tpp) REVERT: G 14 GLU cc_start: 0.7175 (tp30) cc_final: 0.6773 (tp30) REVERT: G 95 MET cc_start: 0.8845 (mtp) cc_final: 0.8603 (mtp) REVERT: G 103 GLN cc_start: 0.8645 (mm110) cc_final: 0.8210 (mp10) REVERT: H 88 ASP cc_start: 0.9119 (m-30) cc_final: 0.8594 (t0) REVERT: H 117 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8076 (mt-10) REVERT: F 32 ARG cc_start: 0.8489 (mtp180) cc_final: 0.8182 (mtp180) REVERT: F 53 ASP cc_start: 0.8976 (p0) cc_final: 0.8768 (p0) REVERT: J 500 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7962 (pt0) outliers start: 121 outliers final: 48 residues processed: 664 average time/residue: 1.2863 time to fit residues: 960.5413 Evaluate side-chains 622 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 564 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLN 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 97 LEU Chi-restraints excluded: chain D residue 25 GLN 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 B residue 67 SER 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 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 M residue 73 CYS Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain T residue 76 LYS 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 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 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 504 LEU Chi-restraints excluded: chain E residue 91 VAL 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 67 SER Chi-restraints excluded: chain H residue 74 HIS Chi-restraints excluded: chain J residue 497 LEU 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 143 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 217 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 72 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 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS O 93 GLN 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 ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3799 r_free = 0.3799 target = 0.119003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093161 restraints weight = 59443.037| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 4.92 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20223 Z= 0.235 Angle : 0.679 10.596 27351 Z= 0.346 Chirality : 0.047 0.243 2905 Planarity : 0.004 0.056 3638 Dihedral : 5.293 57.220 2708 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.95 % Allowed : 27.21 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 2415 helix: 2.10 (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 TRP 0.008 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 PHE 0.022 0.002 PHE I 475 TYR 0.019 0.002 TYR G 20 ARG 0.008 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 909) hydrogen bonds : angle 5.02837 ( 2565) covalent geometry : bond 0.00546 (20223) covalent geometry : angle 0.67937 (27351) *********************** 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 757 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 607 time to evaluate : 2.263 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 5 LYS cc_start: 0.8701 (mtpm) cc_final: 0.8496 (mtpt) REVERT: A 68 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8079 (mm-40) REVERT: A 88 ASP cc_start: 0.8266 (t0) cc_final: 0.7956 (t0) REVERT: A 103 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: C 14 GLU cc_start: 0.7351 (tp30) cc_final: 0.6971 (tp30) REVERT: C 103 GLN cc_start: 0.8948 (mm110) cc_final: 0.8304 (mp10) REVERT: D 13 ARG cc_start: 0.8715 (mmt90) cc_final: 0.8321 (mmm-85) REVERT: D 14 GLU cc_start: 0.9025 (tp30) cc_final: 0.8708 (tp30) REVERT: D 17 ARG cc_start: 0.8824 (ttp80) cc_final: 0.8560 (tmm-80) REVERT: D 93 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7878 (tm-30) REVERT: B 14 GLU cc_start: 0.7747 (tp30) cc_final: 0.7259 (tp30) REVERT: B 50 LYS cc_start: 0.8839 (pttt) cc_final: 0.8620 (mmmt) REVERT: B 66 MET cc_start: 0.8567 (mmm) cc_final: 0.8292 (mmm) REVERT: B 109 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7896 (mmt) REVERT: P 68 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7295 (mt0) REVERT: P 87 ASN cc_start: 0.9356 (m-40) cc_final: 0.9106 (m-40) REVERT: P 103 GLN cc_start: 0.8708 (mm110) cc_final: 0.8331 (mt0) REVERT: P 132 ARG cc_start: 0.7907 (mmt-90) cc_final: 0.7689 (mmt-90) REVERT: N 14 GLU cc_start: 0.7135 (tp30) cc_final: 0.6706 (tp30) REVERT: N 64 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7985 (mmtt) REVERT: N 103 GLN cc_start: 0.8794 (mm110) cc_final: 0.8366 (mp10) REVERT: M 29 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7915 (mtt) REVERT: M 68 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: M 88 ASP cc_start: 0.9114 (m-30) cc_final: 0.8774 (t0) REVERT: O 14 GLU cc_start: 0.7749 (tp30) cc_final: 0.7460 (tp30) REVERT: O 50 LYS cc_start: 0.8694 (pptt) cc_final: 0.8349 (pmtt) REVERT: O 66 MET cc_start: 0.8607 (mmm) cc_final: 0.8259 (mmm) REVERT: O 95 MET cc_start: 0.8841 (mtm) cc_final: 0.8312 (mtp) REVERT: O 123 LYS cc_start: 0.8892 (tppp) cc_final: 0.8623 (tppt) REVERT: T 14 GLU cc_start: 0.8386 (tp30) cc_final: 0.7709 (tp30) REVERT: T 76 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7825 (tptt) REVERT: T 88 ASP cc_start: 0.8497 (t0) cc_final: 0.8222 (t0) REVERT: R 14 GLU cc_start: 0.7184 (tp30) cc_final: 0.6802 (tp30) REVERT: R 36 LYS cc_start: 0.8854 (mptt) cc_final: 0.8475 (mppt) REVERT: R 88 ASP cc_start: 0.8539 (t0) cc_final: 0.8276 (t0) REVERT: R 103 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7948 (mp10) REVERT: Q 25 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: Q 29 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: Q 76 LYS cc_start: 0.8534 (mttt) cc_final: 0.8241 (mttm) REVERT: Q 103 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: S 14 GLU cc_start: 0.7741 (tp30) cc_final: 0.7384 (tp30) REVERT: S 46 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6582 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8818 (pptt) cc_final: 0.8349 (pmtt) REVERT: S 66 MET cc_start: 0.8699 (mmm) cc_final: 0.8357 (mmm) REVERT: S 109 MET cc_start: 0.7867 (mmt) cc_final: 0.7327 (mmt) REVERT: S 110 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: X 500 GLU cc_start: 0.8436 (tt0) cc_final: 0.8094 (tt0) REVERT: X 504 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8057 (mp) REVERT: W 500 GLU cc_start: 0.8519 (tt0) cc_final: 0.8230 (mt-10) REVERT: E 5 LYS cc_start: 0.9095 (mtpm) cc_final: 0.8819 (tttp) REVERT: E 103 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7989 (mt0) REVERT: G 3 MET cc_start: 0.7760 (tpp) cc_final: 0.7372 (tpp) REVERT: G 14 GLU cc_start: 0.7192 (tp30) cc_final: 0.6650 (tp30) REVERT: G 95 MET cc_start: 0.8900 (mtp) cc_final: 0.8688 (mtm) REVERT: G 103 GLN cc_start: 0.8773 (mm110) cc_final: 0.8323 (mp10) REVERT: G 109 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7996 (mtt) REVERT: H 13 ARG cc_start: 0.8613 (mmt90) cc_final: 0.8332 (mmm-85) REVERT: H 88 ASP cc_start: 0.9106 (m-30) cc_final: 0.8604 (t0) REVERT: H 117 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8117 (mt-10) REVERT: F 76 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7619 (mtpt) REVERT: F 109 MET cc_start: 0.7996 (mmt) cc_final: 0.7413 (mmt) REVERT: J 500 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8038 (pt0) outliers start: 150 outliers final: 66 residues processed: 675 average time/residue: 1.2681 time to fit residues: 962.7223 Evaluate side-chains 641 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 560 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 THR Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 75 THR 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 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 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 64 LYS 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 67 SER 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 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 29 MET 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 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 Q residue 103 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 504 LEU Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain E residue 71 THR 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 205 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 C 74 HIS C 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN R 48 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 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN G 37 ASN G 74 HIS G 101 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.119885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095650 restraints weight = 41128.051| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 4.12 r_work: 0.3296 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 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 = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20223 Z= 0.198 Angle : 0.688 10.550 27351 Z= 0.346 Chirality : 0.047 0.251 2905 Planarity : 0.004 0.056 3638 Dihedral : 5.200 57.097 2708 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 6.49 % Allowed : 29.21 % Favored : 64.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2415 helix: 2.11 (0.20), residues: 636 sheet: 0.09 (0.18), residues: 738 loop : 1.13 (0.23), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 PHE 0.024 0.002 PHE I 475 TYR 0.022 0.002 TYR N 40 ARG 0.017 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 909) hydrogen bonds : angle 5.00786 ( 2565) covalent geometry : bond 0.00464 (20223) covalent geometry : angle 0.68756 (27351) *********************** 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 726 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 586 time to evaluate : 2.298 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: 0.8439 (mm-40) cc_final: 0.8216 (mm-40) REVERT: A 88 ASP cc_start: 0.8374 (t0) cc_final: 0.8096 (t0) REVERT: A 134 GLN cc_start: 0.7903 (tt0) cc_final: 0.7536 (tp40) REVERT: C 14 GLU cc_start: 0.7521 (tp30) cc_final: 0.7142 (tp30) REVERT: C 103 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8489 (mm-40) REVERT: D 13 ARG cc_start: 0.8847 (mmt90) cc_final: 0.8455 (mmm-85) REVERT: D 14 GLU cc_start: 0.9067 (tp30) cc_final: 0.8770 (tp30) REVERT: D 17 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8625 (tmm-80) REVERT: D 29 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: B 50 LYS cc_start: 0.8916 (pttt) cc_final: 0.8649 (mmmt) REVERT: B 66 MET cc_start: 0.8728 (mmm) cc_final: 0.8472 (mmm) REVERT: B 95 MET cc_start: 0.8840 (mtm) cc_final: 0.8599 (mtp) REVERT: I 504 LEU cc_start: 0.8992 (mm) cc_final: 0.8791 (mp) REVERT: P 68 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: P 87 ASN cc_start: 0.9386 (m-40) cc_final: 0.9104 (m-40) REVERT: P 103 GLN cc_start: 0.8906 (mm110) cc_final: 0.8616 (mt0) REVERT: N 14 GLU cc_start: 0.7412 (tp30) cc_final: 0.6986 (tp30) REVERT: N 103 GLN cc_start: 0.8912 (mm110) cc_final: 0.8430 (mp10) REVERT: M 14 GLU cc_start: 0.9044 (tp30) cc_final: 0.8824 (tp30) REVERT: M 17 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8771 (ttp80) REVERT: M 29 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8387 (mtt) REVERT: M 32 ARG cc_start: 0.9078 (mmm-85) cc_final: 0.8782 (mmm-85) REVERT: M 68 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: M 88 ASP cc_start: 0.9242 (m-30) cc_final: 0.8876 (t0) REVERT: O 14 GLU cc_start: 0.8121 (tp30) cc_final: 0.7728 (tp30) REVERT: O 50 LYS cc_start: 0.8758 (pptt) cc_final: 0.8375 (pmtt) REVERT: O 66 MET cc_start: 0.8751 (mmm) cc_final: 0.8428 (mmm) REVERT: O 95 MET cc_start: 0.9105 (mtm) cc_final: 0.8566 (mtp) REVERT: O 117 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8379 (mm-30) REVERT: O 123 LYS cc_start: 0.8913 (tppp) cc_final: 0.8691 (tppp) REVERT: T 14 GLU cc_start: 0.8625 (tp30) cc_final: 0.8011 (tp30) REVERT: T 87 ASN cc_start: 0.9134 (m-40) cc_final: 0.8804 (m110) REVERT: T 88 ASP cc_start: 0.8628 (t0) cc_final: 0.8333 (t0) REVERT: R 14 GLU cc_start: 0.7420 (tp30) cc_final: 0.7043 (tp30) REVERT: R 25 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8015 (mm110) REVERT: R 36 LYS cc_start: 0.8871 (mptt) cc_final: 0.8470 (mppt) REVERT: R 88 ASP cc_start: 0.8490 (t0) cc_final: 0.8216 (t0) REVERT: R 103 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8126 (mp10) REVERT: R 109 MET cc_start: 0.8576 (mtt) cc_final: 0.7643 (mtp) REVERT: Q 29 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: Q 68 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7961 (tp40) REVERT: Q 76 LYS cc_start: 0.8606 (mttt) cc_final: 0.8328 (mttm) REVERT: S 14 GLU cc_start: 0.8151 (tp30) cc_final: 0.7799 (tp30) REVERT: S 46 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6540 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8854 (pptt) cc_final: 0.8352 (pmtt) REVERT: S 66 MET cc_start: 0.8806 (mmm) cc_final: 0.8454 (mmm) REVERT: S 109 MET cc_start: 0.8416 (mmt) cc_final: 0.8016 (mmt) REVERT: S 110 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: X 504 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8123 (mp) REVERT: W 500 GLU cc_start: 0.8524 (tt0) cc_final: 0.8320 (mt-10) REVERT: E 5 LYS cc_start: 0.9150 (mtpm) cc_final: 0.8851 (tttp) REVERT: E 103 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8078 (mt0) REVERT: E 136 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: G 1 MET cc_start: 0.6605 (ttt) cc_final: 0.6175 (ttt) REVERT: G 3 MET cc_start: 0.7897 (tpp) cc_final: 0.7501 (tpp) REVERT: G 14 GLU cc_start: 0.7413 (tp30) cc_final: 0.6886 (tp30) REVERT: G 37 ASN cc_start: 0.8290 (t0) cc_final: 0.8088 (t0) REVERT: G 101 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8997 (t0) REVERT: G 103 GLN cc_start: 0.8911 (mm110) cc_final: 0.8614 (mp10) REVERT: H 88 ASP cc_start: 0.9223 (m-30) cc_final: 0.8712 (t0) REVERT: H 117 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8138 (mt-10) REVERT: F 14 GLU cc_start: 0.8002 (tp30) cc_final: 0.7679 (tp30) REVERT: F 76 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7614 (mtpt) REVERT: F 109 MET cc_start: 0.8617 (mmt) cc_final: 0.8178 (mmt) REVERT: J 484 GLU cc_start: 0.8586 (mp0) cc_final: 0.8361 (mp0) REVERT: J 500 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7936 (pt0) outliers start: 140 outliers final: 76 residues processed: 651 average time/residue: 1.3204 time to fit residues: 966.1645 Evaluate side-chains 654 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 565 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL 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 71 THR Chi-restraints excluded: chain C residue 75 THR 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 L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR 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 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 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 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 75 THR Chi-restraints excluded: chain O residue 109 MET Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 117 GLU Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 487 SER 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 T residue 103 GLN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 68 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 38 SER 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 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 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 474 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain E residue 69 ASN 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 70 PHE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 101 ASN Chi-restraints excluded: chain G residue 109 MET 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 67 SER 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 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 130 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 120 optimal weight: 0.0070 chunk 202 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- 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 68 GLN C 72 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** N 24 ASN N 74 HIS M 18 GLN ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN R 37 ASN 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** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.120948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095286 restraints weight = 57169.413| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.85 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20223 Z= 0.175 Angle : 0.688 16.168 27351 Z= 0.344 Chirality : 0.047 0.244 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.099 57.281 2708 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.80 % Allowed : 30.13 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2415 helix: 2.12 (0.20), residues: 636 sheet: 0.06 (0.18), residues: 742 loop : 1.15 (0.23), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 PHE 0.023 0.002 PHE I 475 TYR 0.024 0.001 TYR N 40 ARG 0.009 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 909) hydrogen bonds : angle 4.99731 ( 2565) covalent geometry : bond 0.00409 (20223) covalent geometry : angle 0.68768 (27351) *********************** 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 736 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 611 time to evaluate : 2.418 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 5 LYS cc_start: 0.8690 (mtpm) cc_final: 0.8460 (mtpt) REVERT: A 32 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8284 (mtp180) REVERT: A 87 ASN cc_start: 0.9024 (m-40) cc_final: 0.8736 (m110) REVERT: A 88 ASP cc_start: 0.8293 (t0) cc_final: 0.7922 (t0) REVERT: A 103 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: C 14 GLU cc_start: 0.7250 (tp30) cc_final: 0.6859 (tp30) REVERT: C 63 ARG cc_start: 0.8801 (ttp80) cc_final: 0.8482 (tmm-80) REVERT: C 103 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8486 (mp10) REVERT: D 13 ARG cc_start: 0.8727 (mmt90) cc_final: 0.8321 (mmm-85) REVERT: D 14 GLU cc_start: 0.9032 (tp30) cc_final: 0.8523 (tp30) REVERT: D 17 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8439 (ttp80) REVERT: D 29 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7940 (mtp) REVERT: B 50 LYS cc_start: 0.8843 (pttt) cc_final: 0.8600 (mmmt) REVERT: B 66 MET cc_start: 0.8693 (mmm) cc_final: 0.8436 (mmm) REVERT: B 117 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8466 (mm-30) REVERT: P 68 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7248 (mt0) REVERT: P 81 ASP cc_start: 0.7723 (m-30) cc_final: 0.7271 (t0) REVERT: P 87 ASN cc_start: 0.9320 (m-40) cc_final: 0.8813 (m-40) REVERT: P 88 ASP cc_start: 0.8712 (m-30) cc_final: 0.8062 (t0) REVERT: P 103 GLN cc_start: 0.8694 (mm110) cc_final: 0.8370 (mt0) REVERT: N 14 GLU cc_start: 0.7107 (tp30) cc_final: 0.6657 (tp30) REVERT: N 103 GLN cc_start: 0.8872 (mm110) cc_final: 0.8341 (mm-40) REVERT: M 14 GLU cc_start: 0.8985 (tp30) cc_final: 0.8638 (tp30) REVERT: M 17 ARG cc_start: 0.8845 (ttp80) cc_final: 0.8555 (ttp80) REVERT: M 29 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7957 (mtt) REVERT: M 32 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8597 (mmm-85) REVERT: M 68 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: M 88 ASP cc_start: 0.9073 (m-30) cc_final: 0.8712 (t0) REVERT: M 93 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7629 (tm-30) REVERT: O 14 GLU cc_start: 0.7772 (tp30) cc_final: 0.7484 (tp30) REVERT: O 50 LYS cc_start: 0.8706 (pptt) cc_final: 0.8295 (pmtt) REVERT: O 66 MET cc_start: 0.8684 (mmm) cc_final: 0.8366 (mmm) REVERT: O 95 MET cc_start: 0.8779 (mtm) cc_final: 0.8230 (mtp) REVERT: O 123 LYS cc_start: 0.8892 (tppp) cc_final: 0.8531 (tppt) REVERT: T 5 LYS cc_start: 0.9003 (mtpm) cc_final: 0.8691 (ttmt) REVERT: T 14 GLU cc_start: 0.8386 (tp30) cc_final: 0.7708 (tp30) REVERT: T 87 ASN cc_start: 0.9032 (m-40) cc_final: 0.8690 (m110) REVERT: T 88 ASP cc_start: 0.8503 (t0) cc_final: 0.8138 (t0) REVERT: R 14 GLU cc_start: 0.7138 (tp30) cc_final: 0.6730 (tp30) REVERT: R 25 GLN cc_start: 0.8536 (mm-40) cc_final: 0.7794 (mm110) REVERT: R 36 LYS cc_start: 0.8891 (mptt) cc_final: 0.8500 (mppt) REVERT: R 88 ASP cc_start: 0.8473 (t0) cc_final: 0.8192 (t0) REVERT: R 109 MET cc_start: 0.8279 (mtt) cc_final: 0.7247 (mtp) REVERT: Q 29 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: Q 68 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7833 (tp40) REVERT: Q 76 LYS cc_start: 0.8541 (mttt) cc_final: 0.8316 (mttp) REVERT: S 14 GLU cc_start: 0.7819 (tp30) cc_final: 0.7429 (tp30) REVERT: S 46 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6359 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8785 (pptt) cc_final: 0.8279 (pmtt) REVERT: S 66 MET cc_start: 0.8750 (mmm) cc_final: 0.8382 (mmm) REVERT: S 107 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7660 (mmt90) REVERT: S 109 MET cc_start: 0.7800 (mmt) cc_final: 0.7179 (mmt) REVERT: S 110 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: X 500 GLU cc_start: 0.8469 (tt0) cc_final: 0.8202 (tt0) REVERT: X 504 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8069 (mp) REVERT: E 5 LYS cc_start: 0.9099 (mtpm) cc_final: 0.8803 (tttp) REVERT: E 76 LYS cc_start: 0.8444 (tppt) cc_final: 0.8161 (tptt) REVERT: E 103 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: G 3 MET cc_start: 0.7697 (tpp) cc_final: 0.7322 (tpp) REVERT: G 14 GLU cc_start: 0.7106 (tp30) cc_final: 0.6565 (tp30) REVERT: G 37 ASN cc_start: 0.8285 (t0) cc_final: 0.8038 (t0) REVERT: G 103 GLN cc_start: 0.8983 (mm110) cc_final: 0.8575 (mp10) REVERT: H 14 GLU cc_start: 0.8984 (tp30) cc_final: 0.8558 (tp30) REVERT: H 17 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8416 (ttp80) REVERT: H 88 ASP cc_start: 0.9091 (m-30) cc_final: 0.8581 (t0) REVERT: H 117 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8131 (mt-10) REVERT: F 14 GLU cc_start: 0.7628 (tp30) cc_final: 0.7309 (tp30) REVERT: F 76 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7521 (mtpt) REVERT: F 109 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7565 (mmt) outliers start: 125 outliers final: 63 residues processed: 672 average time/residue: 1.2702 time to fit residues: 960.8000 Evaluate side-chains 644 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 568 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU 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 71 THR Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 75 THR 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 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR 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 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 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 75 THR Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain R residue 41 VAL 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 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 W residue 473 ILE Chi-restraints excluded: chain W residue 474 THR 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 28 ASP 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 474 THR Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain K residue 485 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 100 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 149 optimal weight: 0.0870 chunk 138 optimal weight: 6.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN C 37 ASN C 68 GLN C 74 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN M 37 ASN ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN R 68 GLN R 72 ASN R 74 HIS R 101 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 102 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN E 103 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 87 ASN ** 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 = 0.3843 r_free = 0.3843 target = 0.122427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097699 restraints weight = 50258.949| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.53 r_work: 0.3326 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20223 Z= 0.156 Angle : 0.705 15.296 27351 Z= 0.350 Chirality : 0.047 0.235 2905 Planarity : 0.004 0.069 3638 Dihedral : 5.018 57.099 2708 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.56 % Allowed : 31.48 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2415 helix: 2.15 (0.20), residues: 636 sheet: 0.06 (0.18), residues: 774 loop : 1.14 (0.24), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 509 HIS 0.004 0.001 HIS Q 42 PHE 0.020 0.002 PHE D 112 TYR 0.023 0.001 TYR N 40 ARG 0.011 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 909) hydrogen bonds : angle 4.95798 ( 2565) covalent geometry : bond 0.00364 (20223) covalent geometry : angle 0.70543 (27351) *********************** 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 731 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 611 time to evaluate : 2.291 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: 0.8680 (mtpm) cc_final: 0.8451 (mtpt) REVERT: A 14 GLU cc_start: 0.8493 (tp30) cc_final: 0.7857 (tp30) REVERT: A 87 ASN cc_start: 0.9107 (m-40) cc_final: 0.8839 (m110) REVERT: A 88 ASP cc_start: 0.8381 (t0) cc_final: 0.8017 (t0) REVERT: A 103 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7821 (mt0) REVERT: C 14 GLU cc_start: 0.7504 (tp30) cc_final: 0.7119 (tp30) REVERT: C 36 LYS cc_start: 0.8849 (mptt) cc_final: 0.8605 (mppt) REVERT: C 63 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8488 (tmm-80) REVERT: C 103 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8591 (mm-40) REVERT: C 107 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: D 13 ARG cc_start: 0.8828 (mmt90) cc_final: 0.8428 (mmm-85) REVERT: D 14 GLU cc_start: 0.9076 (tp30) cc_final: 0.8773 (tp30) REVERT: D 17 ARG cc_start: 0.8910 (ttp80) cc_final: 0.8625 (tmm-80) REVERT: D 29 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8286 (mtp) REVERT: B 50 LYS cc_start: 0.8884 (pttt) cc_final: 0.8618 (mmmt) REVERT: B 66 MET cc_start: 0.8809 (mmm) cc_final: 0.8521 (mmm) REVERT: B 109 MET cc_start: 0.8626 (mmt) cc_final: 0.8257 (mmt) REVERT: B 117 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: B 134 GLN cc_start: 0.8525 (tp40) cc_final: 0.8283 (tt0) REVERT: I 475 PHE cc_start: 0.6823 (m-10) cc_final: 0.6508 (m-10) REVERT: I 500 GLU cc_start: 0.8043 (tt0) cc_final: 0.7842 (tt0) REVERT: I 504 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8726 (mp) REVERT: P 5 LYS cc_start: 0.9235 (mtpm) cc_final: 0.8852 (tttp) REVERT: P 68 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7421 (mt0) REVERT: P 81 ASP cc_start: 0.8069 (m-30) cc_final: 0.7467 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9348 (m-40) cc_final: 0.9020 (m-40) REVERT: P 103 GLN cc_start: 0.8902 (mm110) cc_final: 0.8633 (mt0) REVERT: N 14 GLU cc_start: 0.7333 (tp30) cc_final: 0.6914 (tp30) REVERT: N 36 LYS cc_start: 0.8794 (tptp) cc_final: 0.8355 (mppt) REVERT: N 64 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7818 (tmtt) REVERT: N 74 HIS cc_start: 0.7812 (m90) cc_final: 0.7591 (m-70) REVERT: N 88 ASP cc_start: 0.8295 (t0) cc_final: 0.8029 (t0) REVERT: N 103 GLN cc_start: 0.8946 (mm110) cc_final: 0.8583 (mp10) REVERT: N 109 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8633 (mmm) REVERT: M 14 GLU cc_start: 0.9019 (tp30) cc_final: 0.8645 (tp30) REVERT: M 17 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8704 (ttp80) REVERT: M 32 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8689 (mmm-85) REVERT: M 68 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: M 88 ASP cc_start: 0.9218 (m-30) cc_final: 0.8842 (t0) REVERT: O 14 GLU cc_start: 0.8150 (tp30) cc_final: 0.7868 (tp30) REVERT: O 50 LYS cc_start: 0.8746 (pptt) cc_final: 0.8325 (pmtt) REVERT: O 66 MET cc_start: 0.8756 (mmm) cc_final: 0.8385 (mmm) REVERT: O 95 MET cc_start: 0.9019 (mtm) cc_final: 0.8500 (mtp) REVERT: T 5 LYS cc_start: 0.9025 (mtpm) cc_final: 0.8708 (ttmt) REVERT: T 14 GLU cc_start: 0.8631 (tp30) cc_final: 0.8049 (tp30) REVERT: T 87 ASN cc_start: 0.9098 (m-40) cc_final: 0.8760 (m110) REVERT: T 88 ASP cc_start: 0.8585 (t0) cc_final: 0.8193 (t0) REVERT: R 14 GLU cc_start: 0.7386 (tp30) cc_final: 0.6990 (tp30) REVERT: R 25 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7981 (mm110) REVERT: R 36 LYS cc_start: 0.8895 (mptt) cc_final: 0.8491 (mppt) REVERT: R 88 ASP cc_start: 0.8432 (t0) cc_final: 0.8134 (t0) REVERT: R 109 MET cc_start: 0.8192 (mtt) cc_final: 0.7358 (mtp) REVERT: Q 29 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8454 (mtp) REVERT: Q 68 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7728 (tp40) REVERT: S 14 GLU cc_start: 0.8183 (tp30) cc_final: 0.7821 (tp30) REVERT: S 46 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6432 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8843 (pptt) cc_final: 0.8319 (pmtt) REVERT: S 66 MET cc_start: 0.8807 (mmm) cc_final: 0.8548 (mmm) REVERT: S 107 ARG cc_start: 0.8302 (mtt90) cc_final: 0.7837 (mmt90) REVERT: S 109 MET cc_start: 0.8100 (mmt) cc_final: 0.7754 (mmt) REVERT: S 110 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: X 504 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8125 (mp) REVERT: W 500 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8132 (mt-10) REVERT: E 5 LYS cc_start: 0.9132 (mtpm) cc_final: 0.8824 (tttp) REVERT: E 76 LYS cc_start: 0.8586 (tppt) cc_final: 0.7824 (tptt) REVERT: G 1 MET cc_start: 0.6347 (ttt) cc_final: 0.5858 (ttt) REVERT: G 3 MET cc_start: 0.7791 (tpp) cc_final: 0.7403 (tpp) REVERT: G 14 GLU cc_start: 0.7348 (tp30) cc_final: 0.6950 (tp30) REVERT: G 37 ASN cc_start: 0.8370 (t0) cc_final: 0.8109 (t0) REVERT: G 88 ASP cc_start: 0.8281 (t0) cc_final: 0.7962 (t0) REVERT: G 103 GLN cc_start: 0.8989 (mm110) cc_final: 0.8595 (mp10) REVERT: G 109 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7312 (mtt) REVERT: H 13 ARG cc_start: 0.8745 (mmt90) cc_final: 0.8255 (mmm-85) REVERT: H 71 THR cc_start: 0.9008 (t) cc_final: 0.8218 (p) REVERT: H 88 ASP cc_start: 0.9221 (m-30) cc_final: 0.8700 (t0) REVERT: H 117 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8109 (mt-10) REVERT: F 14 GLU cc_start: 0.8072 (tp30) cc_final: 0.7758 (tp30) REVERT: F 76 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7566 (mtpt) REVERT: F 109 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8075 (mmt) outliers start: 120 outliers final: 59 residues processed: 664 average time/residue: 1.2892 time to fit residues: 962.3531 Evaluate side-chains 648 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 575 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 61 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 107 ARG 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 41 VAL 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 117 GLU 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 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 N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 64 LYS 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 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 114 LEU Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain R residue 41 VAL 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 29 MET Chi-restraints excluded: chain Q residue 67 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 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 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 109 MET 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 90 VAL 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 K residue 485 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 214 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 68 GLN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN M 18 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** 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 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.121350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095800 restraints weight = 60955.124| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.96 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20223 Z= 0.180 Angle : 0.723 14.383 27351 Z= 0.359 Chirality : 0.047 0.238 2905 Planarity : 0.004 0.085 3638 Dihedral : 4.969 57.794 2705 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.10 % Allowed : 32.68 % Favored : 62.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 2415 helix: 2.19 (0.20), residues: 628 sheet: 0.04 (0.18), residues: 774 loop : 1.04 (0.23), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 509 HIS 0.004 0.001 HIS E 79 PHE 0.032 0.002 PHE H 15 TYR 0.023 0.002 TYR N 40 ARG 0.021 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 909) hydrogen bonds : angle 5.02620 ( 2565) covalent geometry : bond 0.00423 (20223) covalent geometry : angle 0.72307 (27351) *********************** 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 703 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 593 time to evaluate : 2.100 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: 0.8676 (mtpm) cc_final: 0.8463 (mtpt) REVERT: A 14 GLU cc_start: 0.8326 (tp30) cc_final: 0.7626 (tp30) REVERT: A 87 ASN cc_start: 0.9008 (m-40) cc_final: 0.8733 (m110) REVERT: A 88 ASP cc_start: 0.8367 (t0) cc_final: 0.8018 (t0) REVERT: A 103 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: A 134 GLN cc_start: 0.8450 (tp40) cc_final: 0.8150 (mt0) REVERT: C 14 GLU cc_start: 0.7237 (tp30) cc_final: 0.6835 (tp30) REVERT: C 36 LYS cc_start: 0.8860 (mptt) cc_final: 0.8606 (mppt) REVERT: C 63 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8504 (tmm-80) REVERT: C 103 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8553 (mm-40) REVERT: C 107 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7488 (mtp85) REVERT: D 13 ARG cc_start: 0.8725 (mmt90) cc_final: 0.8310 (mmm-85) REVERT: D 14 GLU cc_start: 0.9039 (tp30) cc_final: 0.8522 (tp30) REVERT: D 17 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8444 (ttp80) REVERT: D 29 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: B 50 LYS cc_start: 0.8828 (pttt) cc_final: 0.8576 (mmmt) REVERT: B 66 MET cc_start: 0.8757 (mmm) cc_final: 0.8456 (mmm) REVERT: B 109 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7460 (mmt) REVERT: B 117 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: I 504 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8810 (mp) REVERT: P 5 LYS cc_start: 0.9225 (mtpm) cc_final: 0.8839 (tttp) REVERT: P 63 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8379 (ttm-80) REVERT: P 68 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7182 (mt0) REVERT: P 81 ASP cc_start: 0.7679 (m-30) cc_final: 0.7270 (t0) REVERT: P 87 ASN cc_start: 0.9298 (m-40) cc_final: 0.8958 (m-40) REVERT: P 103 GLN cc_start: 0.8697 (mm110) cc_final: 0.8442 (mt0) REVERT: P 109 MET cc_start: 0.8597 (ptm) cc_final: 0.8380 (ptm) REVERT: P 117 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8368 (mm-30) REVERT: P 136 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: N 14 GLU cc_start: 0.7096 (tp30) cc_final: 0.6658 (tp30) REVERT: N 74 HIS cc_start: 0.7834 (m90) cc_final: 0.7584 (m-70) REVERT: N 88 ASP cc_start: 0.8398 (t0) cc_final: 0.8125 (t0) REVERT: N 103 GLN cc_start: 0.8901 (mm110) cc_final: 0.8499 (mp10) REVERT: N 109 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8777 (mmm) REVERT: M 14 GLU cc_start: 0.8998 (tp30) cc_final: 0.8782 (tp30) REVERT: M 32 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8572 (mmm-85) REVERT: M 68 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: M 88 ASP cc_start: 0.9064 (m-30) cc_final: 0.8694 (t0) REVERT: O 50 LYS cc_start: 0.8700 (pptt) cc_final: 0.8266 (pmtt) REVERT: O 66 MET cc_start: 0.8698 (mmm) cc_final: 0.8307 (mmm) REVERT: U 500 GLU cc_start: 0.8596 (tt0) cc_final: 0.8101 (tt0) REVERT: T 14 GLU cc_start: 0.8401 (tp30) cc_final: 0.7730 (tp30) REVERT: T 87 ASN cc_start: 0.9002 (m-40) cc_final: 0.8686 (m-40) REVERT: T 88 ASP cc_start: 0.8498 (t0) cc_final: 0.8159 (t0) REVERT: R 14 GLU cc_start: 0.7125 (tp30) cc_final: 0.6723 (tp30) REVERT: R 25 GLN cc_start: 0.8574 (mm-40) cc_final: 0.7878 (mm110) REVERT: R 36 LYS cc_start: 0.8939 (mptt) cc_final: 0.8539 (mppt) REVERT: R 88 ASP cc_start: 0.8441 (t0) cc_final: 0.8147 (t0) REVERT: Q 14 GLU cc_start: 0.8975 (tp30) cc_final: 0.8659 (tp30) REVERT: Q 29 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: Q 68 GLN cc_start: 0.7905 (tp-100) cc_final: 0.7486 (tp40) REVERT: S 14 GLU cc_start: 0.7834 (tp30) cc_final: 0.7438 (tp30) REVERT: S 50 LYS cc_start: 0.8790 (pptt) cc_final: 0.8156 (mmmt) REVERT: S 66 MET cc_start: 0.8762 (mmm) cc_final: 0.8494 (mmm) REVERT: S 109 MET cc_start: 0.7549 (mmt) cc_final: 0.7037 (mmt) REVERT: S 110 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7510 (tt0) REVERT: X 500 GLU cc_start: 0.8433 (tt0) cc_final: 0.8133 (tt0) REVERT: X 504 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8116 (mp) REVERT: W 500 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8205 (mt-10) REVERT: E 5 LYS cc_start: 0.9104 (mtpm) cc_final: 0.8793 (tttp) REVERT: E 76 LYS cc_start: 0.8467 (tppt) cc_final: 0.8171 (tptt) REVERT: G 1 MET cc_start: 0.6185 (ttt) cc_final: 0.5707 (ttt) REVERT: G 3 MET cc_start: 0.7630 (tpp) cc_final: 0.7236 (tpp) REVERT: G 14 GLU cc_start: 0.7082 (tp30) cc_final: 0.6548 (tp30) REVERT: G 37 ASN cc_start: 0.8385 (t0) cc_final: 0.8129 (t0) REVERT: G 88 ASP cc_start: 0.8300 (t0) cc_final: 0.8033 (t0) REVERT: G 103 GLN cc_start: 0.8918 (mm110) cc_final: 0.8397 (mp10) REVERT: G 109 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7092 (mtt) REVERT: H 13 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8268 (mmm-85) REVERT: H 71 THR cc_start: 0.8929 (t) cc_final: 0.8132 (p) REVERT: H 88 ASP cc_start: 0.9059 (m-30) cc_final: 0.8506 (t0) REVERT: H 117 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8250 (mt-10) REVERT: F 14 GLU cc_start: 0.7677 (tp30) cc_final: 0.7432 (tp30) REVERT: F 76 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7517 (mtpt) outliers start: 110 outliers final: 61 residues processed: 641 average time/residue: 1.2802 time to fit residues: 922.6996 Evaluate side-chains 643 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 567 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 41 VAL 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 107 ARG 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 109 MET Chi-restraints excluded: chain B residue 117 GLU 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 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 41 VAL Chi-restraints excluded: chain N residue 67 SER 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 505 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain R residue 41 VAL 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 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 474 THR Chi-restraints excluded: chain W residue 485 SER 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 109 MET 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 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 K residue 485 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 204 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 223 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 210 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 68 GLN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS ** D 68 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN R 74 HIS R 101 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099199 restraints weight = 52932.963| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 4.73 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20223 Z= 0.146 Angle : 0.735 13.863 27351 Z= 0.363 Chirality : 0.047 0.231 2905 Planarity : 0.004 0.054 3638 Dihedral : 4.798 57.171 2705 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.17 % Allowed : 33.70 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2415 helix: 2.18 (0.21), residues: 632 sheet: 0.08 (0.18), residues: 774 loop : 1.09 (0.24), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 509 HIS 0.004 0.001 HIS B 79 PHE 0.026 0.002 PHE H 15 TYR 0.026 0.001 TYR O 125 ARG 0.010 0.001 ARG Q 17 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 909) hydrogen bonds : angle 4.96031 ( 2565) covalent geometry : bond 0.00341 (20223) covalent geometry : angle 0.73520 (27351) *********************** 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 698 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 608 time to evaluate : 2.162 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 5 LYS cc_start: 0.8656 (mtpm) cc_final: 0.8442 (mtpt) REVERT: A 14 GLU cc_start: 0.8327 (tp30) cc_final: 0.7630 (tp30) REVERT: A 87 ASN cc_start: 0.9019 (m-40) cc_final: 0.8699 (m-40) REVERT: A 88 ASP cc_start: 0.8323 (t0) cc_final: 0.7941 (t0) REVERT: A 110 GLN cc_start: 0.8913 (tt0) cc_final: 0.8632 (tt0) REVERT: C 14 GLU cc_start: 0.7253 (tp30) cc_final: 0.6858 (tp30) REVERT: C 36 LYS cc_start: 0.8916 (mptt) cc_final: 0.8662 (mppt) REVERT: C 63 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8505 (tmm-80) REVERT: C 103 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8630 (mm-40) REVERT: D 14 GLU cc_start: 0.9047 (tp30) cc_final: 0.8504 (tp30) REVERT: D 17 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8459 (ttp80) REVERT: D 29 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7807 (mtp) REVERT: B 50 LYS cc_start: 0.8859 (pttt) cc_final: 0.8609 (mmmt) REVERT: B 66 MET cc_start: 0.8739 (mmm) cc_final: 0.8420 (mmm) REVERT: B 109 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7351 (mmt) REVERT: P 5 LYS cc_start: 0.9213 (mtpm) cc_final: 0.8826 (tttp) REVERT: P 63 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8396 (ttm-80) REVERT: P 68 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7107 (mt0) REVERT: P 81 ASP cc_start: 0.7582 (m-30) cc_final: 0.7288 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9311 (m-40) cc_final: 0.8990 (m-40) REVERT: P 103 GLN cc_start: 0.8694 (mm110) cc_final: 0.8438 (mt0) REVERT: P 109 MET cc_start: 0.8613 (ptm) cc_final: 0.8269 (ptm) REVERT: N 14 GLU cc_start: 0.7029 (tp30) cc_final: 0.6591 (tp30) REVERT: N 36 LYS cc_start: 0.8725 (tptp) cc_final: 0.8313 (mppt) REVERT: N 74 HIS cc_start: 0.7814 (m90) cc_final: 0.7556 (m-70) REVERT: N 88 ASP cc_start: 0.8324 (t0) cc_final: 0.8023 (t0) REVERT: N 101 ASN cc_start: 0.8821 (m-40) cc_final: 0.8581 (m110) REVERT: N 103 GLN cc_start: 0.8969 (mm110) cc_final: 0.8536 (mp10) REVERT: M 14 GLU cc_start: 0.8997 (tp30) cc_final: 0.8727 (tp30) REVERT: M 17 ARG cc_start: 0.8864 (ttp80) cc_final: 0.8583 (tmm-80) REVERT: M 29 MET cc_start: 0.8367 (mtp) cc_final: 0.8026 (mtt) REVERT: M 32 ARG cc_start: 0.8952 (mmm-85) cc_final: 0.8504 (mmm-85) REVERT: M 68 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7061 (tm-30) REVERT: M 88 ASP cc_start: 0.8977 (m-30) cc_final: 0.8626 (t0) REVERT: O 50 LYS cc_start: 0.8773 (pptt) cc_final: 0.8324 (pmtt) REVERT: O 66 MET cc_start: 0.8716 (mmm) cc_final: 0.8337 (mmm) REVERT: U 500 GLU cc_start: 0.8658 (tt0) cc_final: 0.8199 (tt0) REVERT: T 5 LYS cc_start: 0.8980 (mtpm) cc_final: 0.8669 (ttmt) REVERT: T 14 GLU cc_start: 0.8447 (tp30) cc_final: 0.7806 (tp30) REVERT: T 76 LYS cc_start: 0.8487 (tptm) cc_final: 0.8028 (tptt) REVERT: T 87 ASN cc_start: 0.8993 (m-40) cc_final: 0.8679 (m110) REVERT: T 88 ASP cc_start: 0.8499 (t0) cc_final: 0.8074 (t0) REVERT: R 14 GLU cc_start: 0.7147 (tp30) cc_final: 0.6749 (tp30) REVERT: R 25 GLN cc_start: 0.8560 (mm-40) cc_final: 0.7824 (mm110) REVERT: R 36 LYS cc_start: 0.8944 (mptt) cc_final: 0.8542 (mppt) REVERT: R 88 ASP cc_start: 0.8369 (t0) cc_final: 0.8052 (t0) REVERT: R 109 MET cc_start: 0.8295 (mtt) cc_final: 0.7692 (mtp) REVERT: Q 29 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7871 (mtt) REVERT: Q 68 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7576 (tp40) REVERT: Q 71 THR cc_start: 0.8760 (t) cc_final: 0.8145 (p) REVERT: S 14 GLU cc_start: 0.7873 (tp30) cc_final: 0.7413 (tp30) REVERT: S 46 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6362 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8864 (pptt) cc_final: 0.8339 (pmtt) REVERT: S 66 MET cc_start: 0.8771 (mmm) cc_final: 0.8478 (mmm) REVERT: S 107 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7700 (mmt90) REVERT: S 109 MET cc_start: 0.7330 (mmt) cc_final: 0.6967 (mmt) REVERT: X 504 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8117 (mp) REVERT: W 500 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8135 (mt-10) REVERT: E 5 LYS cc_start: 0.9106 (mtpm) cc_final: 0.8799 (tttp) REVERT: E 68 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7840 (mm-40) REVERT: E 76 LYS cc_start: 0.8449 (tppt) cc_final: 0.7995 (tptt) REVERT: G 1 MET cc_start: 0.5911 (ttt) cc_final: 0.5483 (ttt) REVERT: G 3 MET cc_start: 0.7484 (tpp) cc_final: 0.7077 (tpp) REVERT: G 14 GLU cc_start: 0.7094 (tp30) cc_final: 0.6660 (tp30) REVERT: G 37 ASN cc_start: 0.8381 (t0) cc_final: 0.8120 (t0) REVERT: G 88 ASP cc_start: 0.8227 (t0) cc_final: 0.7870 (t0) REVERT: G 103 GLN cc_start: 0.8945 (mm110) cc_final: 0.8435 (mp10) REVERT: G 109 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7124 (mtt) REVERT: H 13 ARG cc_start: 0.8625 (mmt90) cc_final: 0.8283 (mmm-85) REVERT: H 71 THR cc_start: 0.8981 (t) cc_final: 0.8220 (p) REVERT: H 88 ASP cc_start: 0.8998 (m-30) cc_final: 0.8436 (t0) REVERT: H 117 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8229 (mt-10) REVERT: F 14 GLU cc_start: 0.7714 (tp30) cc_final: 0.7455 (tp30) REVERT: F 76 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7537 (mtpt) REVERT: F 81 ASP cc_start: 0.8139 (t0) cc_final: 0.7794 (t0) outliers start: 90 outliers final: 48 residues processed: 644 average time/residue: 1.2619 time to fit residues: 914.4325 Evaluate side-chains 636 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 581 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 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 41 VAL 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 109 MET 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 P residue 30 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain N residue 41 VAL 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 M residue 90 VAL Chi-restraints excluded: chain O residue 67 SER 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 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 67 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 X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 485 SER 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 109 MET 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 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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 72 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 134 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 T 110 GLN R 37 ASN ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN R 101 ASN R 134 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.123368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098169 restraints weight = 50149.231| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.58 r_work: 0.3329 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20223 Z= 0.171 Angle : 0.762 13.092 27351 Z= 0.374 Chirality : 0.047 0.241 2905 Planarity : 0.004 0.054 3638 Dihedral : 4.820 56.964 2703 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.99 % Allowed : 34.82 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2415 helix: 1.99 (0.20), residues: 652 sheet: 0.19 (0.19), residues: 694 loop : 1.03 (0.23), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 509 HIS 0.008 0.001 HIS S 79 PHE 0.028 0.002 PHE H 15 TYR 0.025 0.002 TYR O 125 ARG 0.021 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 909) hydrogen bonds : angle 4.97695 ( 2565) covalent geometry : bond 0.00404 (20223) covalent geometry : angle 0.76207 (27351) ********************** 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 670 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 584 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8669 (mtpm) cc_final: 0.8455 (mtpt) REVERT: A 14 GLU cc_start: 0.8524 (tp30) cc_final: 0.7900 (tp30) REVERT: A 87 ASN cc_start: 0.9093 (m-40) cc_final: 0.8839 (m110) REVERT: A 88 ASP cc_start: 0.8415 (t0) cc_final: 0.8060 (t0) REVERT: A 110 GLN cc_start: 0.9188 (tt0) cc_final: 0.8970 (tt0) REVERT: C 14 GLU cc_start: 0.7529 (tp30) cc_final: 0.7136 (tp30) REVERT: C 36 LYS cc_start: 0.8945 (mptt) cc_final: 0.8682 (mppt) REVERT: C 63 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8529 (tmm-80) REVERT: C 103 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8695 (mm-40) REVERT: D 14 GLU cc_start: 0.9105 (tp30) cc_final: 0.8643 (tp30) REVERT: D 17 ARG cc_start: 0.8900 (ttp80) cc_final: 0.8604 (ttp80) REVERT: D 29 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8141 (mtp) REVERT: B 50 LYS cc_start: 0.8834 (pttt) cc_final: 0.8574 (mmmt) REVERT: B 66 MET cc_start: 0.8831 (mmm) cc_final: 0.8505 (mmm) REVERT: B 109 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8248 (mmt) REVERT: B 117 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: P 5 LYS cc_start: 0.9221 (mtpm) cc_final: 0.8833 (tttp) REVERT: P 63 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8523 (ttm-80) REVERT: P 68 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: P 81 ASP cc_start: 0.8029 (m-30) cc_final: 0.7561 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9343 (m-40) cc_final: 0.9015 (m-40) REVERT: P 103 GLN cc_start: 0.8900 (mm110) cc_final: 0.8640 (mt0) REVERT: P 136 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8704 (mt-10) REVERT: N 14 GLU cc_start: 0.7370 (tp30) cc_final: 0.6948 (tp30) REVERT: N 74 HIS cc_start: 0.7779 (m90) cc_final: 0.7483 (m-70) REVERT: N 88 ASP cc_start: 0.8373 (t0) cc_final: 0.8078 (t0) REVERT: N 103 GLN cc_start: 0.9052 (mm110) cc_final: 0.8626 (mp10) REVERT: M 14 GLU cc_start: 0.9062 (tp30) cc_final: 0.8811 (tp30) REVERT: M 17 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8709 (tmm-80) REVERT: M 29 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8378 (mtt) REVERT: M 32 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8596 (mmm-85) REVERT: M 68 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: M 88 ASP cc_start: 0.9196 (m-30) cc_final: 0.8814 (t0) REVERT: O 50 LYS cc_start: 0.8787 (pptt) cc_final: 0.8347 (pmtt) REVERT: O 66 MET cc_start: 0.8781 (mmm) cc_final: 0.8509 (mmm) REVERT: U 500 GLU cc_start: 0.8563 (tt0) cc_final: 0.8037 (tt0) REVERT: T 5 LYS cc_start: 0.8985 (mtpm) cc_final: 0.8658 (ttmt) REVERT: T 14 GLU cc_start: 0.8644 (tp30) cc_final: 0.8079 (tp30) REVERT: T 76 LYS cc_start: 0.8514 (tptm) cc_final: 0.8161 (tptt) REVERT: T 87 ASN cc_start: 0.9086 (m-40) cc_final: 0.8770 (m110) REVERT: T 88 ASP cc_start: 0.8552 (t0) cc_final: 0.8153 (t0) REVERT: R 14 GLU cc_start: 0.7401 (tp30) cc_final: 0.7003 (tp30) REVERT: R 25 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8055 (mm110) REVERT: R 29 MET cc_start: 0.8479 (mmp) cc_final: 0.8139 (mtp) REVERT: R 36 LYS cc_start: 0.8980 (mptt) cc_final: 0.8551 (mppt) REVERT: R 88 ASP cc_start: 0.8417 (t0) cc_final: 0.8087 (t0) REVERT: R 109 MET cc_start: 0.8310 (mtt) cc_final: 0.7516 (mtp) REVERT: Q 17 ARG cc_start: 0.8634 (ptm-80) cc_final: 0.8427 (ptm-80) REVERT: Q 68 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7638 (tp40) REVERT: Q 71 THR cc_start: 0.8885 (t) cc_final: 0.8301 (p) REVERT: S 14 GLU cc_start: 0.8224 (tp30) cc_final: 0.7794 (tp30) REVERT: S 46 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6356 (p0) REVERT: S 50 LYS cc_start: 0.8842 (pptt) cc_final: 0.8311 (pmtt) REVERT: S 66 MET cc_start: 0.8823 (mmm) cc_final: 0.8533 (mmm) REVERT: S 107 ARG cc_start: 0.8330 (mtt90) cc_final: 0.7917 (mmt90) REVERT: S 109 MET cc_start: 0.8035 (mmt) cc_final: 0.7820 (mmt) REVERT: X 504 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8132 (mp) REVERT: W 500 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8206 (mt-10) REVERT: E 5 LYS cc_start: 0.9102 (mtpm) cc_final: 0.8776 (tttp) REVERT: E 14 GLU cc_start: 0.8514 (tp30) cc_final: 0.8062 (tp30) REVERT: E 68 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7978 (mm-40) REVERT: E 76 LYS cc_start: 0.8553 (tppt) cc_final: 0.8259 (tptt) REVERT: G 3 MET cc_start: 0.7656 (tpp) cc_final: 0.7204 (tpp) REVERT: G 14 GLU cc_start: 0.7365 (tp30) cc_final: 0.6945 (tp30) REVERT: G 37 ASN cc_start: 0.8494 (t0) cc_final: 0.8248 (t0) REVERT: G 88 ASP cc_start: 0.8275 (t0) cc_final: 0.7941 (t0) REVERT: G 103 GLN cc_start: 0.8997 (mm110) cc_final: 0.8485 (mp10) REVERT: G 109 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7273 (mtt) REVERT: G 117 GLU cc_start: 0.9123 (tt0) cc_final: 0.8899 (tt0) REVERT: H 13 ARG cc_start: 0.8759 (mmt90) cc_final: 0.8435 (mmm-85) REVERT: H 71 THR cc_start: 0.9051 (t) cc_final: 0.8357 (p) REVERT: H 74 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (m-70) REVERT: H 88 ASP cc_start: 0.9165 (m-30) cc_final: 0.8586 (t0) REVERT: H 117 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8173 (mt-10) REVERT: F 14 GLU cc_start: 0.8121 (tp30) cc_final: 0.7877 (tp30) REVERT: F 76 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7563 (mtpt) REVERT: F 81 ASP cc_start: 0.8341 (t0) cc_final: 0.8039 (t0) outliers start: 86 outliers final: 48 residues processed: 625 average time/residue: 1.2580 time to fit residues: 884.5101 Evaluate side-chains 626 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 567 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 72 ASN Chi-restraints excluded: chain C residue 75 THR 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 41 VAL 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 109 MET Chi-restraints excluded: chain B residue 117 GLU 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 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 67 SER 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 M residue 90 VAL Chi-restraints excluded: chain O residue 67 SER 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 R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 67 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 X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 485 SER 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 109 MET 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 74 HIS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 181 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 HIS R 101 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.123348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097836 restraints weight = 54939.661| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.78 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.159 20223 Z= 0.216 Angle : 0.890 59.199 27351 Z= 0.472 Chirality : 0.048 0.609 2905 Planarity : 0.004 0.052 3638 Dihedral : 4.908 57.015 2703 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Rotamer: Outliers : 3.99 % Allowed : 34.77 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.18), residues: 2415 helix: 2.01 (0.20), residues: 652 sheet: 0.19 (0.19), residues: 694 loop : 1.02 (0.23), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 509 HIS 0.007 0.001 HIS S 79 PHE 0.024 0.002 PHE H 15 TYR 0.023 0.001 TYR N 40 ARG 0.028 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 909) hydrogen bonds : angle 4.97983 ( 2565) covalent geometry : bond 0.00470 (20223) covalent geometry : angle 0.89009 (27351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17490.96 seconds wall clock time: 300 minutes 50.67 seconds (18050.67 seconds total)