Starting phenix.real_space_refine on Tue Jun 17 04:58:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivr_60933/06_2025/9ivr_60933.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivr_60933/06_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_60933/06_2025/9ivr_60933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivr_60933/06_2025/9ivr_60933.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivr_60933/06_2025/9ivr_60933.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivr_60933/06_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-5710/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: 12.18, 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: 4.52 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: 2.40 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: 6.14 Time building geometry restraints manager: 5.41 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 44.290 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.080 ------------------------------------------------------------------------------- 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 : 2.205 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: 1.3102 time to fit residues: 987.7256 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 : 2.182 ------------------------------------------------------------------------------- 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 = 0.098900 restraints weight = 50968.037| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 4.69 r_work: 0.3346 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- 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 : 2.445 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: 0.8158 (mm-40) REVERT: A 103 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: C 14 GLU cc_start: 0.7543 (tp30) cc_final: 0.7205 (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: 0.9088 (mmm-85) cc_final: 0.8857 (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: 0.7679 (tp30) REVERT: B 46 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7119 (OUTLIER) REVERT: B 50 LYS cc_start: 0.8933 (pttt) cc_final: 0.8635 (pmtt) REVERT: B 53 ASP cc_start: 0.9111 (p0) cc_final: 0.8895 (p0) REVERT: I 500 GLU cc_start: 0.7967 (tt0) cc_final: 0.7736 (tt0) REVERT: P 29 MET cc_start: 0.8565 (mmp) cc_final: 0.8344 (mmm) REVERT: P 81 ASP cc_start: 0.8145 (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: 0.8776 (m-30) cc_final: 0.8162 (t0) REVERT: N 14 GLU cc_start: 0.7461 (tp30) cc_final: 0.7090 (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: 0.8203 (mtt) REVERT: M 68 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8046 (pp30) REVERT: M 76 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8380 (mttt) REVERT: M 88 ASP cc_start: 0.9253 (m-30) cc_final: 0.8922 (t0) REVERT: O 14 GLU cc_start: 0.8214 (tp30) cc_final: 0.7869 (tp30) REVERT: O 50 LYS cc_start: 0.8464 (pptt) cc_final: 0.8177 (mmmt) REVERT: O 53 ASP cc_start: 0.9103 (p0) cc_final: 0.8876 (p0) REVERT: V 474 THR cc_start: 0.8486 (p) cc_final: 0.8097 (t) REVERT: U 500 GLU cc_start: 0.8512 (tt0) cc_final: 0.8233 (tt0) REVERT: T 14 GLU cc_start: 0.8559 (tp30) cc_final: 0.7971 (tp30) REVERT: T 53 ASP cc_start: 0.8810 (p0) cc_final: 0.8600 (p0) REVERT: T 76 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8103 (tptp) REVERT: R 14 GLU cc_start: 0.7435 (tp30) cc_final: 0.7105 (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: 0.8094 (mm-40) cc_final: 0.7851 (mm-40) REVERT: R 109 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8099 (mtp) REVERT: Q 14 GLU cc_start: 0.9069 (tp30) cc_final: 0.8846 (tp30) REVERT: Q 17 ARG cc_start: 0.8872 (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: 0.7458 (t0) cc_final: 0.7127 (t0) REVERT: S 14 GLU cc_start: 0.8031 (tp30) cc_final: 0.7697 (tp30) REVERT: S 46 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6879 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8823 (pptt) cc_final: 0.8417 (pmtt) REVERT: S 53 ASP cc_start: 0.9042 (p0) cc_final: 0.8806 (p0) REVERT: S 109 MET cc_start: 0.8161 (mmt) cc_final: 0.7840 (mmt) REVERT: X 504 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7966 (mp) REVERT: X 506 ASP cc_start: 0.7185 (t0) cc_final: 0.6866 (t0) REVERT: W 500 GLU cc_start: 0.8552 (tt0) cc_final: 0.8156 (mt-10) REVERT: E 5 LYS cc_start: 0.9195 (mtpm) cc_final: 0.8954 (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: 0.9265 (m-30) cc_final: 0.8759 (t0) REVERT: F 14 GLU cc_start: 0.8077 (tp30) cc_final: 0.7863 (tp30) REVERT: F 53 ASP cc_start: 0.8995 (p0) cc_final: 0.8758 (p0) REVERT: J 500 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7748 (pt0) outliers start: 111 outliers final: 44 residues processed: 672 average time/residue: 1.3280 time to fit residues: 1004.4705 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 : 2.359 ------------------------------------------------------------------------------- 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: 10.0000 chunk 213 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 210 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 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 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094960 restraints weight = 59331.520| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 5.03 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3450 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3450 r_free = 0.3450 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 = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20223 Z= 0.204 Angle : 0.664 10.093 27351 Z= 0.336 Chirality : 0.047 0.191 2905 Planarity : 0.004 0.050 3638 Dihedral : 5.215 64.041 2708 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.56 % Allowed : 27.21 % 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: 1.52 (0.19), residues: 2415 helix: 2.20 (0.20), residues: 636 sheet: 0.13 (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 0.022 0.002 PHE H 15 TYR 0.019 0.002 TYR G 20 ARG 0.016 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 909) hydrogen bonds : angle 5.00452 ( 2565) covalent geometry : bond 0.00475 (20223) covalent geometry : angle 0.66438 (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 719 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 599 time to evaluate : 2.397 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: 0.8701 (mtpm) cc_final: 0.8449 (mtpt) REVERT: A 29 MET cc_start: 0.8601 (mmp) cc_final: 0.8153 (mmm) REVERT: A 88 ASP cc_start: 0.8013 (t0) cc_final: 0.7784 (t0) REVERT: A 103 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: C 14 GLU cc_start: 0.7335 (tp30) cc_final: 0.6943 (tp30) REVERT: C 103 GLN cc_start: 0.8912 (mm110) cc_final: 0.8494 (mm-40) REVERT: D 13 ARG cc_start: 0.8717 (mmt90) cc_final: 0.8326 (mmm-85) REVERT: D 14 GLU cc_start: 0.9032 (tp30) cc_final: 0.8809 (tp30) REVERT: D 17 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8530 (ttp80) REVERT: B 14 GLU cc_start: 0.7710 (tp30) cc_final: 0.7441 (tp30) REVERT: B 50 LYS cc_start: 0.8887 (pttt) cc_final: 0.8647 (mmmt) REVERT: B 109 MET cc_start: 0.8286 (mmt) cc_final: 0.7996 (mmt) REVERT: P 68 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7235 (mt0) REVERT: P 81 ASP cc_start: 0.7790 (m-30) cc_final: 0.7200 (t0) REVERT: P 87 ASN cc_start: 0.9367 (m-40) cc_final: 0.9127 (m-40) REVERT: P 103 GLN cc_start: 0.8717 (mm110) cc_final: 0.8440 (mt0) REVERT: P 132 ARG cc_start: 0.7885 (mmt-90) cc_final: 0.7625 (mmt-90) REVERT: N 14 GLU cc_start: 0.7164 (tp30) cc_final: 0.6725 (tp30) REVERT: N 60 GLU cc_start: 0.6731 (pp20) cc_final: 0.6522 (pp20) REVERT: N 103 GLN cc_start: 0.8669 (mm110) cc_final: 0.8207 (mp10) REVERT: M 29 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7804 (mtt) REVERT: M 68 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: M 76 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8292 (mttt) REVERT: M 88 ASP cc_start: 0.9099 (m-30) cc_final: 0.8750 (t0) REVERT: M 109 MET cc_start: 0.8039 (ptm) cc_final: 0.7798 (ttt) REVERT: O 14 GLU cc_start: 0.7794 (tp30) cc_final: 0.7549 (tp30) REVERT: O 50 LYS cc_start: 0.8697 (pptt) cc_final: 0.8453 (pmtt) REVERT: O 53 ASP cc_start: 0.9011 (p0) cc_final: 0.8802 (p0) REVERT: O 66 MET cc_start: 0.8476 (mmm) cc_final: 0.8225 (mmm) REVERT: O 95 MET cc_start: 0.8828 (mtm) cc_final: 0.8343 (mtp) REVERT: O 123 LYS cc_start: 0.8846 (tppp) cc_final: 0.8608 (tppp) REVERT: V 474 THR cc_start: 0.8533 (p) cc_final: 0.8079 (t) REVERT: T 14 GLU cc_start: 0.8357 (tp30) cc_final: 0.7688 (tp30) REVERT: T 29 MET cc_start: 0.8587 (mmp) cc_final: 0.8373 (mmm) REVERT: T 76 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7913 (tptp) REVERT: T 88 ASP cc_start: 0.8370 (t0) cc_final: 0.8158 (t0) REVERT: R 14 GLU cc_start: 0.7272 (tp30) cc_final: 0.6873 (tp30) REVERT: R 25 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7904 (mm110) REVERT: R 36 LYS cc_start: 0.8770 (mptt) cc_final: 0.8396 (mppt) REVERT: R 103 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7909 (mp10) REVERT: Q 17 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8521 (ttp80) REVERT: Q 29 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: Q 68 GLN cc_start: 0.8299 (tp40) cc_final: 0.7910 (tp40) REVERT: S 14 GLU cc_start: 0.7722 (tp30) cc_final: 0.7297 (tp30) REVERT: S 46 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6623 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8805 (pptt) cc_final: 0.8362 (pmtt) REVERT: S 53 ASP cc_start: 0.9028 (p0) cc_final: 0.8808 (p0) REVERT: S 66 MET cc_start: 0.8606 (mmm) cc_final: 0.8357 (mmm) REVERT: S 109 MET cc_start: 0.7756 (mmt) cc_final: 0.7184 (mmt) REVERT: S 110 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: X 504 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7982 (mp) REVERT: W 500 GLU cc_start: 0.8512 (tt0) cc_final: 0.8217 (mt-10) REVERT: E 5 LYS cc_start: 0.9145 (mtpm) cc_final: 0.8917 (tttp) REVERT: E 103 GLN cc_start: 0.8523 (mm110) cc_final: 0.7952 (mt0) REVERT: G 1 MET cc_start: 0.6383 (ttt) cc_final: 0.6165 (ttt) REVERT: G 3 MET cc_start: 0.7500 (tpp) cc_final: 0.7104 (tpp) REVERT: G 14 GLU cc_start: 0.7177 (tp30) cc_final: 0.6776 (tp30) REVERT: G 95 MET cc_start: 0.8845 (mtp) cc_final: 0.8603 (mtp) REVERT: G 103 GLN cc_start: 0.8640 (mm110) cc_final: 0.8205 (mp10) REVERT: H 88 ASP cc_start: 0.9127 (m-30) cc_final: 0.8598 (t0) REVERT: H 117 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8072 (mt-10) REVERT: F 32 ARG cc_start: 0.8493 (mtp180) cc_final: 0.8185 (mtp180) REVERT: F 53 ASP cc_start: 0.8975 (p0) cc_final: 0.8767 (p0) REVERT: J 500 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7936 (pt0) outliers start: 120 outliers final: 48 residues processed: 659 average time/residue: 1.2768 time to fit residues: 947.0697 Evaluate side-chains 616 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 559 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 28 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain 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 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 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 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 91 VAL 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 F residue 109 MET 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: 0.9980 chunk 91 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 217 optimal weight: 0.0050 chunk 54 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- 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 72 ASN D 68 GLN ** D 69 ASN ** 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 74 HIS M 18 GLN M 37 ASN O 24 ASN T 68 GLN T 110 GLN R 68 GLN R 72 ASN R 74 HIS R 101 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 102 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 127 HIS E 128 ASN 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 122 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 = 0.3871 r_free = 0.3871 target = 0.124214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097890 restraints weight = 58667.854| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 5.02 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20223 Z= 0.142 Angle : 0.644 10.018 27351 Z= 0.323 Chirality : 0.046 0.227 2905 Planarity : 0.004 0.053 3638 Dihedral : 4.990 56.042 2708 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.07 % Allowed : 27.58 % Favored : 66.34 % 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: 1.61 (0.19), residues: 2415 helix: 2.29 (0.20), residues: 632 sheet: 0.19 (0.19), residues: 738 loop : 1.19 (0.23), residues: 1045 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 0.021 0.002 PHE I 475 TYR 0.021 0.001 TYR N 40 ARG 0.007 0.001 ARG H 32 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 909) hydrogen bonds : angle 4.83675 ( 2565) covalent geometry : bond 0.00327 (20223) covalent geometry : angle 0.64437 (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 769 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 638 time to evaluate : 2.380 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 14 GLU cc_start: 0.8262 (tp30) cc_final: 0.7584 (tp30) REVERT: A 29 MET cc_start: 0.8615 (mmp) cc_final: 0.8183 (mmm) REVERT: A 68 GLN cc_start: 0.8349 (mm110) cc_final: 0.8146 (mm-40) REVERT: A 88 ASP cc_start: 0.8034 (t0) cc_final: 0.7780 (t0) REVERT: A 134 GLN cc_start: 0.7630 (tt0) cc_final: 0.7207 (tt0) REVERT: C 14 GLU cc_start: 0.7288 (tp30) cc_final: 0.6882 (tp30) REVERT: C 101 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8471 (m110) REVERT: C 103 GLN cc_start: 0.8978 (mm110) cc_final: 0.8411 (mp10) REVERT: C 107 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7433 (mtm-85) REVERT: C 109 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: D 14 GLU cc_start: 0.9022 (tp30) cc_final: 0.8713 (tp30) REVERT: D 17 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8537 (ttp80) REVERT: D 29 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8015 (mtp) REVERT: D 93 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7705 (tm-30) REVERT: D 134 GLN cc_start: 0.7639 (tm-30) cc_final: 0.7409 (tm-30) REVERT: B 14 GLU cc_start: 0.7744 (tp30) cc_final: 0.7285 (tp30) REVERT: B 50 LYS cc_start: 0.8836 (pttt) cc_final: 0.8636 (mmmt) REVERT: B 109 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7836 (mmt) REVERT: P 68 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7192 (mt0) REVERT: P 81 ASP cc_start: 0.7694 (m-30) cc_final: 0.7210 (t0) REVERT: P 87 ASN cc_start: 0.9382 (m-40) cc_final: 0.9179 (m-40) REVERT: P 103 GLN cc_start: 0.8683 (mm110) cc_final: 0.8415 (mt0) REVERT: N 14 GLU cc_start: 0.7118 (tp30) cc_final: 0.6646 (tp30) REVERT: N 103 GLN cc_start: 0.8783 (mm110) cc_final: 0.8263 (mp10) REVERT: N 109 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8283 (mmt) REVERT: M 29 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7972 (mtt) REVERT: M 76 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8269 (mttt) REVERT: M 88 ASP cc_start: 0.9057 (m-30) cc_final: 0.8715 (t0) REVERT: O 14 GLU cc_start: 0.7831 (tp30) cc_final: 0.7518 (tp30) REVERT: O 50 LYS cc_start: 0.8692 (pptt) cc_final: 0.8340 (pmtt) REVERT: O 66 MET cc_start: 0.8588 (mmm) cc_final: 0.8309 (mmm) REVERT: O 95 MET cc_start: 0.8817 (mtm) cc_final: 0.8282 (mtp) REVERT: O 123 LYS cc_start: 0.8890 (tppp) cc_final: 0.8648 (tppp) REVERT: V 474 THR cc_start: 0.8606 (p) cc_final: 0.8130 (t) REVERT: T 14 GLU cc_start: 0.8385 (tp30) cc_final: 0.7726 (tp30) REVERT: T 76 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7834 (tptt) REVERT: T 88 ASP cc_start: 0.8407 (t0) cc_final: 0.8144 (t0) REVERT: T 103 GLN cc_start: 0.8763 (mm110) cc_final: 0.8554 (mt0) REVERT: R 14 GLU cc_start: 0.7149 (tp30) cc_final: 0.6736 (tp30) REVERT: R 24 ASN cc_start: 0.8813 (t0) cc_final: 0.8593 (t0) REVERT: R 36 LYS cc_start: 0.8812 (mptt) cc_final: 0.8429 (mppt) REVERT: R 88 ASP cc_start: 0.8407 (t0) cc_final: 0.8112 (t0) REVERT: R 103 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8004 (mp10) REVERT: R 109 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8084 (mtp) REVERT: Q 29 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8189 (mtt) REVERT: Q 68 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7789 (tp40) REVERT: S 14 GLU cc_start: 0.7757 (tp30) cc_final: 0.7296 (tp30) REVERT: S 46 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.6533 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8846 (pptt) cc_final: 0.8360 (pmtt) REVERT: S 53 ASP cc_start: 0.8986 (p0) cc_final: 0.8774 (p0) REVERT: S 66 MET cc_start: 0.8707 (mmm) cc_final: 0.8390 (mmm) REVERT: S 109 MET cc_start: 0.7637 (mmt) cc_final: 0.7015 (mmt) REVERT: S 110 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7491 (tt0) REVERT: X 504 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8008 (mp) REVERT: W 500 GLU cc_start: 0.8563 (tt0) cc_final: 0.8330 (mt-10) REVERT: E 5 LYS cc_start: 0.9121 (mtpm) cc_final: 0.8897 (tttp) REVERT: E 103 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: G 3 MET cc_start: 0.7451 (tpp) cc_final: 0.7055 (tpp) REVERT: G 14 GLU cc_start: 0.7139 (tp30) cc_final: 0.6708 (tp30) REVERT: G 37 ASN cc_start: 0.8223 (t0) cc_final: 0.8003 (t0) REVERT: G 95 MET cc_start: 0.8872 (mtp) cc_final: 0.8665 (mtp) REVERT: G 103 GLN cc_start: 0.8780 (mm110) cc_final: 0.8389 (mp10) REVERT: G 109 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7446 (mtt) REVERT: H 13 ARG cc_start: 0.8610 (mmt90) cc_final: 0.8325 (mmm-85) REVERT: H 32 ARG cc_start: 0.9173 (mmm-85) cc_final: 0.8933 (mmm-85) REVERT: H 88 ASP cc_start: 0.9086 (m-30) cc_final: 0.8566 (t0) REVERT: H 117 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8036 (mt-10) REVERT: F 53 ASP cc_start: 0.8969 (p0) cc_final: 0.8754 (p0) REVERT: F 76 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7582 (mtpt) REVERT: F 109 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: J 500 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7910 (pt0) outliers start: 131 outliers final: 48 residues processed: 696 average time/residue: 1.2627 time to fit residues: 992.0802 Evaluate side-chains 646 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 580 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 114 LEU 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 C residue 101 ASN Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 114 LEU 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 N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 109 MET 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 73 CYS Chi-restraints excluded: chain O residue 41 VAL Chi-restraints excluded: chain O residue 114 LEU 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 71 THR 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 29 MET Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain 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 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 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 205 optimal weight: 0.0270 chunk 75 optimal weight: 0.3980 chunk 19 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.6844 ------------------------------------------------------------------------------- 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 74 HIS C 103 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 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** P 110 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 72 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS O 93 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 110 GLN R 48 ASN R 68 GLN R 72 ASN R 74 HIS R 101 ASN S 37 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 110 GLN G 74 HIS G 101 ASN ** 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 122 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 = 0.3808 r_free = 0.3808 target = 0.119691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095291 restraints weight = 41224.555| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 4.15 r_work: 0.3301 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.085 | | 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) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20223 Z= 0.221 Angle : 0.694 10.077 27351 Z= 0.349 Chirality : 0.047 0.245 2905 Planarity : 0.004 0.067 3638 Dihedral : 5.181 56.949 2708 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.21 % Allowed : 28.98 % Favored : 64.81 % 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 (0.18), residues: 2415 helix: 2.12 (0.20), residues: 636 sheet: 0.13 (0.18), residues: 738 loop : 1.17 (0.23), residues: 1041 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 0.033 0.002 PHE H 15 TYR 0.024 0.002 TYR N 40 ARG 0.017 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 909) hydrogen bonds : angle 5.00491 ( 2565) covalent geometry : bond 0.00516 (20223) covalent geometry : angle 0.69360 (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 728 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 594 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8480 (mm110) cc_final: 0.8210 (mm-40) REVERT: A 88 ASP cc_start: 0.8295 (t0) cc_final: 0.7994 (t0) REVERT: A 134 GLN cc_start: 0.7714 (tt0) cc_final: 0.7452 (tt0) REVERT: C 14 GLU cc_start: 0.7523 (tp30) cc_final: 0.7125 (tp30) REVERT: C 103 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8484 (mm-40) REVERT: C 109 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8406 (mtp) REVERT: D 14 GLU cc_start: 0.9046 (tp30) cc_final: 0.8824 (tp30) REVERT: D 17 ARG cc_start: 0.8922 (ttp80) cc_final: 0.8722 (ttp80) REVERT: D 29 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8362 (mtp) REVERT: B 50 LYS cc_start: 0.8840 (pttt) cc_final: 0.8618 (mmmt) REVERT: B 66 MET cc_start: 0.8632 (mmm) cc_final: 0.8375 (mmm) REVERT: P 68 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: P 76 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8390 (tptm) REVERT: P 81 ASP cc_start: 0.8145 (m-30) cc_final: 0.7464 (t0) REVERT: P 87 ASN cc_start: 0.9369 (m-40) cc_final: 0.8937 (m-40) REVERT: P 88 ASP cc_start: 0.8840 (m-30) cc_final: 0.8034 (t0) REVERT: P 103 GLN cc_start: 0.8901 (mm110) cc_final: 0.8642 (mt0) REVERT: N 14 GLU cc_start: 0.7407 (tp30) cc_final: 0.6981 (tp30) REVERT: N 60 GLU cc_start: 0.7227 (pp20) cc_final: 0.6980 (pp20) REVERT: N 74 HIS cc_start: 0.7774 (m90) cc_final: 0.7508 (m-70) REVERT: N 103 GLN cc_start: 0.8923 (mm110) cc_final: 0.8463 (mp10) REVERT: N 109 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8366 (mmt) REVERT: M 14 GLU cc_start: 0.9032 (tp30) cc_final: 0.8754 (tp30) REVERT: M 17 ARG cc_start: 0.8886 (tmm-80) cc_final: 0.8685 (ttp80) REVERT: M 25 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: M 29 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8371 (mtt) REVERT: M 76 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8416 (mttt) REVERT: M 88 ASP cc_start: 0.9253 (m-30) cc_final: 0.8881 (t0) REVERT: M 109 MET cc_start: 0.8291 (ptm) cc_final: 0.8053 (ttt) REVERT: O 14 GLU cc_start: 0.8095 (tp30) cc_final: 0.7712 (tp30) REVERT: O 50 LYS cc_start: 0.8715 (pptt) cc_final: 0.8319 (pmtt) REVERT: O 66 MET cc_start: 0.8745 (mmm) cc_final: 0.8432 (mmm) REVERT: O 95 MET cc_start: 0.9079 (mtm) cc_final: 0.8548 (mtp) REVERT: O 123 LYS cc_start: 0.8893 (tppp) cc_final: 0.8682 (tppp) REVERT: T 14 GLU cc_start: 0.8600 (tp30) cc_final: 0.7976 (tp30) REVERT: T 76 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7937 (tptt) REVERT: T 87 ASN cc_start: 0.9106 (m-40) cc_final: 0.8791 (m110) REVERT: T 88 ASP cc_start: 0.8564 (t0) cc_final: 0.8272 (t0) REVERT: T 103 GLN cc_start: 0.8969 (mm110) cc_final: 0.8416 (mt0) REVERT: R 14 GLU cc_start: 0.7403 (tp30) cc_final: 0.7016 (tp30) REVERT: R 29 MET cc_start: 0.8463 (mmp) cc_final: 0.8135 (mtp) REVERT: R 36 LYS cc_start: 0.8852 (mptt) cc_final: 0.8441 (mppt) REVERT: R 88 ASP cc_start: 0.8523 (t0) cc_final: 0.8282 (t0) REVERT: R 109 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8393 (mtp) REVERT: Q 25 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: Q 29 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8496 (mtp) REVERT: S 14 GLU cc_start: 0.8146 (tp30) cc_final: 0.7785 (tp30) REVERT: S 46 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.6484 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8832 (pptt) cc_final: 0.8336 (pmtt) REVERT: S 66 MET cc_start: 0.8797 (mmm) cc_final: 0.8443 (mmm) REVERT: S 109 MET cc_start: 0.8401 (mmt) cc_final: 0.7997 (mmt) REVERT: S 110 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: X 500 GLU cc_start: 0.8445 (tt0) cc_final: 0.8119 (tt0) REVERT: X 504 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8040 (mp) REVERT: W 500 GLU cc_start: 0.8505 (tt0) cc_final: 0.8291 (mt-10) REVERT: E 5 LYS cc_start: 0.9159 (mtpm) cc_final: 0.8857 (tttp) REVERT: E 103 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8386 (mt0) REVERT: G 1 MET cc_start: 0.6550 (ttt) cc_final: 0.6067 (ttt) REVERT: G 3 MET cc_start: 0.7783 (tpp) cc_final: 0.7394 (tpp) REVERT: G 14 GLU cc_start: 0.7388 (tp30) cc_final: 0.6850 (tp30) REVERT: G 37 ASN cc_start: 0.8398 (t0) cc_final: 0.8167 (t0) REVERT: G 69 ASN cc_start: 0.8708 (p0) cc_final: 0.8482 (p0) REVERT: G 101 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8967 (t0) REVERT: G 103 GLN cc_start: 0.8911 (mm110) cc_final: 0.8629 (mp10) REVERT: G 109 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7984 (mtt) REVERT: H 14 GLU cc_start: 0.8975 (tp30) cc_final: 0.8721 (tp30) REVERT: H 29 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: H 32 ARG cc_start: 0.9269 (mmm-85) cc_final: 0.9030 (mmm-85) REVERT: H 88 ASP cc_start: 0.9231 (m-30) cc_final: 0.8727 (t0) REVERT: H 117 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7998 (mt-10) REVERT: F 14 GLU cc_start: 0.7992 (tp30) cc_final: 0.7658 (tp30) REVERT: F 76 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7644 (mtpt) REVERT: J 500 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7985 (pt0) outliers start: 134 outliers final: 64 residues processed: 659 average time/residue: 1.3233 time to fit residues: 980.1494 Evaluate side-chains 650 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 567 time to evaluate : 2.500 ------------------------------------------------------------------------------- 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 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain 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 I residue 485 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 91 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 N residue 109 MET 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 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 75 THR 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 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 R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN 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 97 LEU Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain Q residue 39 SER Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 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 29 MET Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 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: 1.9990 chunk 122 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 chunk 202 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 68 GLN C 72 ASN D 37 ASN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 72 ASN 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 110 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN R 68 GLN R 72 ASN R 101 ASN Q 68 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** 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 68 GLN ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.120527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.094943 restraints weight = 57089.724| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 4.84 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20223 Z= 0.186 Angle : 0.686 9.669 27351 Z= 0.344 Chirality : 0.047 0.244 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.086 56.434 2708 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.70 % Allowed : 30.60 % Favored : 63.70 % 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: 1.48 (0.18), residues: 2415 helix: 2.12 (0.20), residues: 636 sheet: 0.12 (0.18), residues: 738 loop : 1.15 (0.23), residues: 1041 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 0.026 0.002 PHE H 15 TYR 0.024 0.002 TYR N 40 ARG 0.010 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 909) hydrogen bonds : angle 4.96988 ( 2565) covalent geometry : bond 0.00435 (20223) covalent geometry : angle 0.68581 (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 726 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 603 time to evaluate : 2.402 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: 0.8370 (mm110) cc_final: 0.8108 (mm-40) REVERT: A 88 ASP cc_start: 0.8262 (t0) cc_final: 0.7960 (t0) REVERT: A 103 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: A 134 GLN cc_start: 0.7478 (tt0) cc_final: 0.6909 (tt0) REVERT: C 14 GLU cc_start: 0.7288 (tp30) cc_final: 0.6880 (tp30) REVERT: C 63 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8515 (tmm-80) REVERT: C 103 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8490 (mp10) REVERT: C 109 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8252 (mtp) REVERT: D 13 ARG cc_start: 0.8726 (mmt90) cc_final: 0.8314 (mmm-85) REVERT: D 14 GLU cc_start: 0.9014 (tp30) cc_final: 0.8736 (tp30) REVERT: D 17 ARG cc_start: 0.8798 (ttp80) cc_final: 0.8566 (ttp80) REVERT: D 29 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7961 (mtp) REVERT: D 93 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7686 (tm-30) REVERT: B 50 LYS cc_start: 0.8810 (pttt) cc_final: 0.8597 (mmmt) REVERT: B 66 MET cc_start: 0.8602 (mmm) cc_final: 0.8315 (mmm) REVERT: P 5 LYS cc_start: 0.9277 (mtpp) cc_final: 0.8952 (tttp) REVERT: P 32 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7105 (mtp180) REVERT: P 68 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: P 81 ASP cc_start: 0.7772 (m-30) cc_final: 0.7308 (t0) REVERT: P 87 ASN cc_start: 0.9323 (m-40) cc_final: 0.9022 (m-40) REVERT: P 103 GLN cc_start: 0.8690 (mm110) cc_final: 0.8411 (mt0) REVERT: P 132 ARG cc_start: 0.7866 (mmt-90) cc_final: 0.7640 (mmt-90) REVERT: N 14 GLU cc_start: 0.7110 (tp30) cc_final: 0.6671 (tp30) REVERT: N 68 GLN cc_start: 0.7708 (mt0) cc_final: 0.7226 (mp10) REVERT: N 74 HIS cc_start: 0.7766 (m90) cc_final: 0.7493 (m-70) REVERT: N 103 GLN cc_start: 0.8808 (mm110) cc_final: 0.8291 (mp10) REVERT: N 109 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8290 (mmt) REVERT: M 14 GLU cc_start: 0.8968 (tp30) cc_final: 0.8669 (tp30) REVERT: M 25 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: M 29 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7920 (mtt) REVERT: M 32 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8586 (mmm-85) REVERT: M 68 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8075 (pp30) REVERT: M 76 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8316 (mttt) REVERT: M 88 ASP cc_start: 0.9073 (m-30) cc_final: 0.8711 (t0) REVERT: O 14 GLU cc_start: 0.7793 (tp30) cc_final: 0.7543 (tp30) REVERT: O 50 LYS cc_start: 0.8692 (pptt) cc_final: 0.8282 (pmtt) REVERT: O 66 MET cc_start: 0.8679 (mmm) cc_final: 0.8368 (mmm) REVERT: O 95 MET cc_start: 0.8798 (mtm) cc_final: 0.8195 (mtp) REVERT: V 495 ASP cc_start: 0.8533 (m-30) cc_final: 0.8096 (p0) REVERT: T 14 GLU cc_start: 0.8396 (tp30) cc_final: 0.7732 (tp30) REVERT: T 76 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7778 (tptt) REVERT: T 87 ASN cc_start: 0.9026 (m-40) cc_final: 0.8697 (m-40) REVERT: T 88 ASP cc_start: 0.8499 (t0) cc_final: 0.8191 (t0) REVERT: T 103 GLN cc_start: 0.8828 (mm110) cc_final: 0.8264 (mt0) REVERT: R 14 GLU cc_start: 0.7126 (tp30) cc_final: 0.6705 (tp30) REVERT: R 25 GLN cc_start: 0.8523 (mm-40) cc_final: 0.7690 (mm110) REVERT: R 29 MET cc_start: 0.8425 (mmp) cc_final: 0.8081 (mtp) REVERT: R 36 LYS cc_start: 0.8902 (mptt) cc_final: 0.8498 (mppt) REVERT: R 88 ASP cc_start: 0.8505 (t0) cc_final: 0.8222 (t0) REVERT: R 109 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: Q 29 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: Q 68 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: S 14 GLU cc_start: 0.7808 (tp30) cc_final: 0.7415 (tp30) REVERT: S 46 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6328 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8825 (pptt) cc_final: 0.8314 (pmtt) REVERT: S 66 MET cc_start: 0.8743 (mmm) cc_final: 0.8378 (mmm) REVERT: S 109 MET cc_start: 0.7767 (mmt) cc_final: 0.7199 (mmt) REVERT: S 110 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: X 504 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8028 (mp) REVERT: E 5 LYS cc_start: 0.9093 (mtpm) cc_final: 0.8792 (tttp) REVERT: E 76 LYS cc_start: 0.8465 (tppp) cc_final: 0.8129 (tptt) REVERT: E 103 GLN cc_start: 0.8325 (mm110) cc_final: 0.8002 (mt0) REVERT: G 1 MET cc_start: 0.6376 (ttt) cc_final: 0.5993 (ttt) REVERT: G 3 MET cc_start: 0.7623 (tpp) cc_final: 0.7229 (tpp) REVERT: G 14 GLU cc_start: 0.7100 (tp30) cc_final: 0.6695 (tp30) REVERT: G 37 ASN cc_start: 0.8345 (t0) cc_final: 0.8115 (t0) REVERT: G 95 MET cc_start: 0.8802 (mtp) cc_final: 0.8594 (mtm) REVERT: G 103 GLN cc_start: 0.8959 (mm110) cc_final: 0.8553 (mp10) REVERT: G 109 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.6303 (mtt) REVERT: H 13 ARG cc_start: 0.8624 (mmt90) cc_final: 0.8334 (mmm-85) REVERT: H 32 ARG cc_start: 0.9166 (mmm-85) cc_final: 0.8882 (mmm-85) REVERT: H 71 THR cc_start: 0.8951 (t) cc_final: 0.8147 (p) REVERT: H 88 ASP cc_start: 0.9071 (m-30) cc_final: 0.8557 (t0) REVERT: H 109 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.6675 (tpt) REVERT: H 117 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8219 (mt-10) REVERT: F 76 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7542 (mtpt) REVERT: F 109 MET cc_start: 0.7640 (mmt) cc_final: 0.7286 (mmt) REVERT: J 500 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8019 (pt0) outliers start: 123 outliers final: 69 residues processed: 660 average time/residue: 1.3216 time to fit residues: 980.2588 Evaluate side-chains 656 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 570 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain 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 C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain 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 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 67 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 109 MET 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 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 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 R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 109 MET 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 53 ASP Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 110 GLN Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 474 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 28 ASP 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 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 37 ASN C 68 GLN C 74 HIS ** 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** M 18 GLN O 24 ASN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 110 GLN R 68 GLN R 72 ASN R 74 HIS R 101 ASN Q 68 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN G 74 HIS G 101 ASN ** 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.097896 restraints weight = 49906.741| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.60 r_work: 0.3338 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20223 Z= 0.149 Angle : 0.697 10.892 27351 Z= 0.347 Chirality : 0.046 0.231 2905 Planarity : 0.004 0.067 3638 Dihedral : 4.946 56.380 2708 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.38 % Allowed : 32.31 % Favored : 62.31 % 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: 1.54 (0.19), residues: 2415 helix: 2.18 (0.21), residues: 636 sheet: 0.16 (0.18), residues: 738 loop : 1.16 (0.23), residues: 1041 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 0.020 0.002 PHE H 15 TYR 0.021 0.001 TYR N 40 ARG 0.012 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 909) hydrogen bonds : angle 4.89098 ( 2565) covalent geometry : bond 0.00347 (20223) covalent geometry : angle 0.69704 (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 732 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 616 time to evaluate : 2.326 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 14 GLU cc_start: 0.8495 (tp30) cc_final: 0.7863 (tp30) REVERT: A 68 GLN cc_start: 0.8461 (mm110) cc_final: 0.8232 (mm-40) REVERT: A 88 ASP cc_start: 0.8335 (t0) cc_final: 0.8028 (t0) REVERT: A 134 GLN cc_start: 0.7626 (tt0) cc_final: 0.7285 (tp40) REVERT: C 14 GLU cc_start: 0.7513 (tp30) cc_final: 0.7124 (tp30) REVERT: C 63 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8498 (tmm-80) REVERT: C 101 ASN cc_start: 0.8980 (m-40) cc_final: 0.8691 (m110) REVERT: C 103 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8618 (mm-40) REVERT: C 109 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8373 (mtp) REVERT: D 13 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8444 (mmm-85) REVERT: D 14 GLU cc_start: 0.9051 (tp30) cc_final: 0.8757 (tp30) REVERT: D 17 ARG cc_start: 0.8881 (ttp80) cc_final: 0.8593 (ttp80) REVERT: D 29 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: D 93 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 66 MET cc_start: 0.8753 (mmm) cc_final: 0.8450 (mmm) REVERT: I 475 PHE cc_start: 0.6550 (m-10) cc_final: 0.6124 (m-10) REVERT: I 500 GLU cc_start: 0.8039 (tt0) cc_final: 0.7830 (tt0) REVERT: I 504 LEU cc_start: 0.8941 (mm) cc_final: 0.8727 (mp) REVERT: P 5 LYS cc_start: 0.9268 (mtpp) cc_final: 0.8952 (tttp) REVERT: P 68 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7362 (mt0) REVERT: P 81 ASP cc_start: 0.7996 (m-30) cc_final: 0.7490 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9346 (m-40) cc_final: 0.9043 (m-40) REVERT: P 103 GLN cc_start: 0.8886 (mm110) cc_final: 0.8610 (mt0) REVERT: N 14 GLU cc_start: 0.7362 (tp30) cc_final: 0.6930 (tp30) REVERT: N 36 LYS cc_start: 0.8818 (tptp) cc_final: 0.8335 (mppt) REVERT: N 58 GLN cc_start: 0.7590 (tt0) cc_final: 0.7379 (tt0) REVERT: N 60 GLU cc_start: 0.7327 (pp20) cc_final: 0.7114 (pp20) REVERT: N 63 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8414 (ttm-80) REVERT: N 74 HIS cc_start: 0.7803 (m90) cc_final: 0.7569 (m-70) REVERT: N 88 ASP cc_start: 0.8271 (t0) cc_final: 0.8021 (t0) REVERT: N 103 GLN cc_start: 0.8924 (mm110) cc_final: 0.8470 (mm-40) REVERT: M 17 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8722 (ttp-110) REVERT: M 29 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8344 (mtt) REVERT: M 32 ARG cc_start: 0.9048 (mmm-85) cc_final: 0.8683 (mmm-85) REVERT: M 68 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8094 (pp30) REVERT: M 88 ASP cc_start: 0.9203 (m-30) cc_final: 0.8823 (t0) REVERT: O 14 GLU cc_start: 0.8178 (tp30) cc_final: 0.7903 (tp30) REVERT: O 50 LYS cc_start: 0.8719 (pptt) cc_final: 0.8291 (pmtt) REVERT: O 66 MET cc_start: 0.8760 (mmm) cc_final: 0.8393 (mmm) REVERT: U 500 GLU cc_start: 0.8489 (tt0) cc_final: 0.7960 (tt0) REVERT: T 5 LYS cc_start: 0.8984 (mtpm) cc_final: 0.8666 (ttmt) REVERT: T 14 GLU cc_start: 0.8645 (tp30) cc_final: 0.8054 (tp30) REVERT: T 87 ASN cc_start: 0.9094 (m-40) cc_final: 0.8760 (m-40) REVERT: T 88 ASP cc_start: 0.8580 (t0) cc_final: 0.8211 (t0) REVERT: R 14 GLU cc_start: 0.7377 (tp30) cc_final: 0.6971 (tp30) REVERT: R 25 GLN cc_start: 0.8685 (mm-40) cc_final: 0.7873 (mm110) REVERT: R 29 MET cc_start: 0.8459 (mmp) cc_final: 0.7913 (mtp) REVERT: R 36 LYS cc_start: 0.8967 (mptt) cc_final: 0.8523 (mppt) REVERT: R 88 ASP cc_start: 0.8413 (t0) cc_final: 0.8108 (t0) REVERT: R 109 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8439 (mtp) REVERT: Q 17 ARG cc_start: 0.8823 (ttp80) cc_final: 0.8532 (ttp80) REVERT: Q 29 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8562 (mtt) REVERT: Q 68 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7978 (tp40) REVERT: S 14 GLU cc_start: 0.8184 (tp30) cc_final: 0.7750 (tp30) REVERT: S 46 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6398 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8846 (pptt) cc_final: 0.8321 (pmtt) REVERT: S 66 MET cc_start: 0.8798 (mmm) cc_final: 0.8444 (mmm) REVERT: S 107 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7729 (mmt90) REVERT: S 109 MET cc_start: 0.7960 (mmt) cc_final: 0.7599 (mmt) REVERT: X 500 GLU cc_start: 0.8427 (tt0) cc_final: 0.8138 (tt0) REVERT: X 504 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7984 (mp) REVERT: W 500 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8119 (mt-10) REVERT: E 5 LYS cc_start: 0.9115 (mtpm) cc_final: 0.8798 (tttp) REVERT: E 76 LYS cc_start: 0.8609 (tppp) cc_final: 0.7873 (tptt) REVERT: E 103 GLN cc_start: 0.8533 (mm110) cc_final: 0.8271 (mt0) REVERT: G 1 MET cc_start: 0.6357 (ttt) cc_final: 0.6047 (ttt) REVERT: G 3 MET cc_start: 0.7726 (tpp) cc_final: 0.7338 (tpp) REVERT: G 14 GLU cc_start: 0.7356 (tp30) cc_final: 0.6955 (tp30) REVERT: G 29 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: G 37 ASN cc_start: 0.8424 (t0) cc_final: 0.8162 (t0) REVERT: G 88 ASP cc_start: 0.8296 (t0) cc_final: 0.7970 (t0) REVERT: G 103 GLN cc_start: 0.8955 (mm110) cc_final: 0.8558 (mp10) REVERT: G 109 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.6601 (mtt) REVERT: H 32 ARG cc_start: 0.9252 (mmm-85) cc_final: 0.8987 (mmm-85) REVERT: H 71 THR cc_start: 0.9040 (t) cc_final: 0.8306 (p) REVERT: H 88 ASP cc_start: 0.9206 (m-30) cc_final: 0.8683 (t0) REVERT: H 109 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7004 (tpt) REVERT: H 117 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8183 (mt-10) REVERT: F 76 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7554 (mtpt) REVERT: F 81 ASP cc_start: 0.8391 (t0) cc_final: 0.8144 (t0) REVERT: F 109 MET cc_start: 0.8503 (mmt) cc_final: 0.8099 (mmt) REVERT: F 123 LYS cc_start: 0.8859 (tppt) cc_final: 0.8631 (tppt) REVERT: J 500 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7995 (pt0) outliers start: 116 outliers final: 64 residues processed: 667 average time/residue: 1.3212 time to fit residues: 991.4283 Evaluate side-chains 657 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 581 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 61 ILE 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 C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 474 THR Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 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 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 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 67 SER Chi-restraints excluded: chain M residue 73 CYS 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 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 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 29 MET Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 68 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 29 MET 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 67 SER Chi-restraints excluded: chain H residue 74 HIS Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 506 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 68 GLN C 72 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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** O 68 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN T 103 GLN T 110 GLN R 37 ASN R 68 GLN R 72 ASN R 101 ASN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN E 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN G 74 HIS G 101 ASN ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.120090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094082 restraints weight = 61104.942| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 4.99 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20223 Z= 0.209 Angle : 0.721 11.130 27351 Z= 0.363 Chirality : 0.048 0.242 2905 Planarity : 0.005 0.084 3638 Dihedral : 4.953 57.803 2705 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.42 % Allowed : 32.59 % Favored : 61.98 % 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: 2.08 (0.20), residues: 636 sheet: 0.13 (0.18), residues: 738 loop : 1.11 (0.23), residues: 1041 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 0.026 0.002 PHE H 15 TYR 0.022 0.002 TYR N 40 ARG 0.021 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 909) hydrogen bonds : angle 5.00956 ( 2565) covalent geometry : bond 0.00491 (20223) covalent geometry : angle 0.72142 (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 708 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 591 time to evaluate : 2.173 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 32 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8010 (mtp180) REVERT: A 87 ASN cc_start: 0.8992 (m-40) cc_final: 0.8703 (m110) REVERT: A 88 ASP cc_start: 0.8307 (t0) cc_final: 0.8005 (t0) REVERT: A 103 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: A 134 GLN cc_start: 0.7422 (tt0) cc_final: 0.7068 (tt0) REVERT: C 14 GLU cc_start: 0.7267 (tp30) cc_final: 0.6866 (tp30) REVERT: C 36 LYS cc_start: 0.8819 (mptt) cc_final: 0.8583 (mppt) REVERT: C 63 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8498 (tmm-80) REVERT: C 103 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8567 (mm-40) REVERT: C 109 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: D 13 ARG cc_start: 0.8746 (mmt90) cc_final: 0.8322 (mmm-85) REVERT: D 14 GLU cc_start: 0.9028 (tp30) cc_final: 0.8726 (tp30) REVERT: D 17 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8565 (ttp80) REVERT: D 29 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: D 93 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 50 LYS cc_start: 0.8811 (pttt) cc_final: 0.8578 (mmmt) REVERT: B 66 MET cc_start: 0.8714 (mmm) cc_final: 0.8439 (mmm) REVERT: L 484 GLU cc_start: 0.8981 (mp0) cc_final: 0.8642 (mp0) REVERT: L 500 GLU cc_start: 0.8497 (tt0) cc_final: 0.8277 (tt0) REVERT: I 504 LEU cc_start: 0.9000 (mm) cc_final: 0.8799 (mp) REVERT: P 5 LYS cc_start: 0.9268 (mtpp) cc_final: 0.8941 (tttp) REVERT: P 68 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: P 81 ASP cc_start: 0.7756 (m-30) cc_final: 0.7348 (t0) REVERT: P 87 ASN cc_start: 0.9312 (m-40) cc_final: 0.8982 (m-40) REVERT: P 103 GLN cc_start: 0.8695 (mm110) cc_final: 0.8408 (mt0) REVERT: N 14 GLU cc_start: 0.7098 (tp30) cc_final: 0.6651 (tp30) REVERT: N 60 GLU cc_start: 0.7423 (pp20) cc_final: 0.7172 (pp20) REVERT: N 74 HIS cc_start: 0.7857 (m90) cc_final: 0.7593 (m-70) REVERT: N 88 ASP cc_start: 0.8429 (t0) cc_final: 0.8147 (t0) REVERT: N 103 GLN cc_start: 0.8887 (mm110) cc_final: 0.8474 (mp10) REVERT: M 32 ARG cc_start: 0.8954 (mmm-85) cc_final: 0.8527 (mmm-85) REVERT: M 68 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7961 (pp30) REVERT: M 88 ASP cc_start: 0.9065 (m-30) cc_final: 0.8697 (t0) REVERT: O 50 LYS cc_start: 0.8682 (pptt) cc_final: 0.8259 (pmtt) REVERT: O 66 MET cc_start: 0.8705 (mmm) cc_final: 0.8355 (mmm) REVERT: T 14 GLU cc_start: 0.8406 (tp30) cc_final: 0.7750 (tp30) REVERT: T 87 ASN cc_start: 0.9017 (m-40) cc_final: 0.8690 (m-40) REVERT: T 88 ASP cc_start: 0.8502 (t0) cc_final: 0.8203 (t0) REVERT: T 103 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: R 14 GLU cc_start: 0.7120 (tp30) cc_final: 0.6702 (tp30) REVERT: R 25 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8247 (mm110) REVERT: R 29 MET cc_start: 0.8426 (mmp) cc_final: 0.7842 (mtp) REVERT: R 36 LYS cc_start: 0.8935 (mptt) cc_final: 0.8536 (mppt) REVERT: R 74 HIS cc_start: 0.7574 (m90) cc_final: 0.7371 (m90) REVERT: R 88 ASP cc_start: 0.8480 (t0) cc_final: 0.8205 (t0) REVERT: Q 29 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8016 (mtp) REVERT: Q 68 GLN cc_start: 0.8277 (tp-100) cc_final: 0.7747 (mt0) REVERT: S 14 GLU cc_start: 0.7822 (tp30) cc_final: 0.7422 (tp30) REVERT: S 46 ASP cc_start: 0.7213 (OUTLIER) cc_final: 0.6336 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8792 (pptt) cc_final: 0.8281 (pmtt) REVERT: S 66 MET cc_start: 0.8755 (mmm) cc_final: 0.8529 (mmm) REVERT: S 109 MET cc_start: 0.7690 (mmt) cc_final: 0.7244 (mmt) REVERT: S 110 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: X 500 GLU cc_start: 0.8342 (tt0) cc_final: 0.8074 (tt0) REVERT: X 504 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7989 (mp) REVERT: W 500 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8202 (mt-10) REVERT: E 5 LYS cc_start: 0.9106 (mtpm) cc_final: 0.8793 (tttp) REVERT: E 68 GLN cc_start: 0.8142 (mm110) cc_final: 0.7899 (mm-40) REVERT: E 76 LYS cc_start: 0.8459 (tppp) cc_final: 0.7985 (tptp) REVERT: E 103 GLN cc_start: 0.8409 (mm110) cc_final: 0.8093 (mt0) REVERT: G 3 MET cc_start: 0.7611 (tpp) cc_final: 0.7219 (tpp) REVERT: G 14 GLU cc_start: 0.7100 (tp30) cc_final: 0.6566 (tp30) REVERT: G 29 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8163 (mtp) REVERT: G 37 ASN cc_start: 0.8415 (t0) cc_final: 0.8176 (t0) REVERT: G 69 ASN cc_start: 0.8677 (p0) cc_final: 0.8384 (p0) REVERT: G 88 ASP cc_start: 0.8327 (t0) cc_final: 0.8076 (t0) REVERT: G 101 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8838 (t0) REVERT: G 103 GLN cc_start: 0.8898 (mm110) cc_final: 0.8385 (mp10) REVERT: G 117 GLU cc_start: 0.9025 (tt0) cc_final: 0.8794 (tt0) REVERT: H 17 ARG cc_start: 0.8516 (ptm-80) cc_final: 0.8301 (ptm-80) REVERT: H 32 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8801 (mmm-85) REVERT: H 71 THR cc_start: 0.8929 (t) cc_final: 0.8164 (p) REVERT: H 88 ASP cc_start: 0.9083 (m-30) cc_final: 0.8575 (t0) REVERT: H 117 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8201 (mt-10) REVERT: F 76 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7525 (mtpt) REVERT: F 81 ASP cc_start: 0.8269 (t0) cc_final: 0.7958 (t0) REVERT: J 500 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: J 502 ASP cc_start: 0.8448 (m-30) cc_final: 0.8228 (m-30) outliers start: 117 outliers final: 68 residues processed: 644 average time/residue: 1.3519 time to fit residues: 979.2495 Evaluate side-chains 647 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 567 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 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 C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain 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 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 P residue 91 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 60 GLU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain 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 T residue 103 GLN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN 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 28 ASP 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 53 ASP 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 G residue 7 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 29 MET 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 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 F residue 76 LYS Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 204 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 222 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 185 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 37 ASN C 68 GLN C 72 ASN C 74 HIS ** 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 24 ASN N 48 ASN 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 103 GLN R 68 GLN R 72 ASN R 101 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN G 74 HIS G 101 ASN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.125078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.099540 restraints weight = 52726.233| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 4.72 r_work: 0.3366 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20223 Z= 0.142 Angle : 0.722 11.802 27351 Z= 0.361 Chirality : 0.047 0.230 2905 Planarity : 0.004 0.055 3638 Dihedral : 4.763 56.580 2703 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.99 % Allowed : 34.49 % Favored : 61.52 % 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: 2.20 (0.20), residues: 632 sheet: 0.18 (0.18), residues: 738 loop : 1.13 (0.23), residues: 1045 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 0.019 0.002 PHE M 15 TYR 0.021 0.001 TYR N 40 ARG 0.012 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 909) hydrogen bonds : angle 4.96004 ( 2565) covalent geometry : bond 0.00330 (20223) covalent geometry : angle 0.72223 (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 704 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 618 time to evaluate : 2.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8509 (tp30) cc_final: 0.7882 (tp30) REVERT: A 87 ASN cc_start: 0.9078 (m-40) cc_final: 0.8739 (m-40) REVERT: A 88 ASP cc_start: 0.8338 (t0) cc_final: 0.8019 (t0) REVERT: A 134 GLN cc_start: 0.7598 (tt0) cc_final: 0.7325 (tp40) REVERT: C 14 GLU cc_start: 0.7506 (tp30) cc_final: 0.7118 (tp30) REVERT: C 36 LYS cc_start: 0.8904 (mptt) cc_final: 0.8645 (mppt) REVERT: C 63 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8513 (tmm-80) REVERT: C 101 ASN cc_start: 0.8921 (m-40) cc_final: 0.8575 (m110) REVERT: C 103 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8690 (mm-40) REVERT: C 109 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: D 13 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8467 (mmm-85) REVERT: D 14 GLU cc_start: 0.9094 (tp30) cc_final: 0.8795 (tp30) REVERT: D 17 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8566 (ttp80) REVERT: D 29 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: B 50 LYS cc_start: 0.8833 (pttt) cc_final: 0.8577 (mmmt) REVERT: B 66 MET cc_start: 0.8763 (mmm) cc_final: 0.8454 (mmm) REVERT: L 484 GLU cc_start: 0.8923 (mp0) cc_final: 0.8563 (mp0) REVERT: I 500 GLU cc_start: 0.8064 (tt0) cc_final: 0.7839 (tt0) REVERT: I 504 LEU cc_start: 0.9008 (mm) cc_final: 0.8779 (mp) REVERT: P 5 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8928 (tttp) REVERT: P 68 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7264 (mt0) REVERT: P 81 ASP cc_start: 0.7982 (m-30) cc_final: 0.7630 (OUTLIER) REVERT: P 87 ASN cc_start: 0.9374 (m-40) cc_final: 0.9063 (m-40) REVERT: P 103 GLN cc_start: 0.8896 (mm110) cc_final: 0.8646 (mt0) REVERT: P 110 GLN cc_start: 0.9195 (tt0) cc_final: 0.8901 (tt0) REVERT: N 14 GLU cc_start: 0.7309 (tp30) cc_final: 0.6878 (tp30) REVERT: N 36 LYS cc_start: 0.8758 (tptp) cc_final: 0.8338 (mppt) REVERT: N 73 CYS cc_start: 0.7779 (p) cc_final: 0.7558 (p) REVERT: N 74 HIS cc_start: 0.7857 (m90) cc_final: 0.7571 (m-70) REVERT: N 88 ASP cc_start: 0.8331 (t0) cc_final: 0.8040 (t0) REVERT: N 103 GLN cc_start: 0.8995 (mm110) cc_final: 0.8564 (mp10) REVERT: N 109 MET cc_start: 0.8506 (mmt) cc_final: 0.8272 (mmt) REVERT: M 29 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8301 (mtt) REVERT: M 32 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8623 (mmm-85) REVERT: M 68 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7607 (pp30) REVERT: M 70 PHE cc_start: 0.8849 (m-80) cc_final: 0.8630 (m-80) REVERT: M 88 ASP cc_start: 0.9169 (m-30) cc_final: 0.8783 (t0) REVERT: O 50 LYS cc_start: 0.8716 (pptt) cc_final: 0.8276 (pmtt) REVERT: O 66 MET cc_start: 0.8749 (mmm) cc_final: 0.8373 (mmm) REVERT: U 500 GLU cc_start: 0.8541 (tt0) cc_final: 0.8069 (tt0) REVERT: T 5 LYS cc_start: 0.8975 (mtpm) cc_final: 0.8661 (ttmt) REVERT: T 14 GLU cc_start: 0.8658 (tp30) cc_final: 0.8059 (tp30) REVERT: T 87 ASN cc_start: 0.9095 (m-40) cc_final: 0.8762 (m-40) REVERT: T 88 ASP cc_start: 0.8546 (t0) cc_final: 0.8141 (t0) REVERT: R 1 MET cc_start: 0.6591 (ptm) cc_final: 0.6387 (ptm) REVERT: R 14 GLU cc_start: 0.7381 (tp30) cc_final: 0.6972 (tp30) REVERT: R 25 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8403 (mm110) REVERT: R 29 MET cc_start: 0.8434 (mmp) cc_final: 0.7881 (mtp) REVERT: R 36 LYS cc_start: 0.8983 (mptt) cc_final: 0.8534 (mppt) REVERT: R 48 ASN cc_start: 0.8684 (t0) cc_final: 0.8372 (t0) REVERT: R 88 ASP cc_start: 0.8399 (t0) cc_final: 0.8072 (t0) REVERT: Q 13 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8459 (mmm-85) REVERT: Q 29 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8248 (mtt) REVERT: Q 68 GLN cc_start: 0.8382 (tp-100) cc_final: 0.7868 (tp40) REVERT: Q 71 THR cc_start: 0.8754 (t) cc_final: 0.8193 (p) REVERT: Q 136 GLU cc_start: 0.8840 (pt0) cc_final: 0.8353 (pp20) REVERT: S 14 GLU cc_start: 0.8221 (tp30) cc_final: 0.7802 (tp30) REVERT: S 46 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.6376 (OUTLIER) REVERT: S 50 LYS cc_start: 0.8837 (pptt) cc_final: 0.8305 (pmtt) REVERT: S 66 MET cc_start: 0.8798 (mmm) cc_final: 0.8513 (mmm) REVERT: S 109 MET cc_start: 0.7946 (mmt) cc_final: 0.7744 (mmt) REVERT: X 500 GLU cc_start: 0.8484 (tt0) cc_final: 0.8197 (tt0) REVERT: X 504 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8019 (mp) REVERT: W 500 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8139 (mt-10) REVERT: E 5 LYS cc_start: 0.9112 (mtpm) cc_final: 0.8791 (tttp) REVERT: E 76 LYS cc_start: 0.8555 (tppp) cc_final: 0.8275 (tptt) REVERT: E 103 GLN cc_start: 0.8525 (mm110) cc_final: 0.8252 (mt0) REVERT: G 3 MET cc_start: 0.7668 (tpp) cc_final: 0.7234 (tpp) REVERT: G 14 GLU cc_start: 0.7325 (tp30) cc_final: 0.6923 (tp30) REVERT: G 37 ASN cc_start: 0.8437 (t0) cc_final: 0.8175 (t0) REVERT: G 69 ASN cc_start: 0.8726 (p0) cc_final: 0.8456 (p0) REVERT: G 88 ASP cc_start: 0.8256 (t0) cc_final: 0.7899 (t0) REVERT: G 101 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8866 (t0) REVERT: G 103 GLN cc_start: 0.9062 (mm110) cc_final: 0.8649 (mp10) REVERT: G 117 GLU cc_start: 0.9126 (tt0) cc_final: 0.8904 (tt0) REVERT: H 32 ARG cc_start: 0.9229 (mmm-85) cc_final: 0.8940 (mmm-85) REVERT: H 71 THR cc_start: 0.9051 (t) cc_final: 0.8356 (p) REVERT: H 88 ASP cc_start: 0.9184 (m-30) cc_final: 0.8631 (t0) REVERT: H 117 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8199 (mt-10) REVERT: F 50 LYS cc_start: 0.8824 (tttt) cc_final: 0.8583 (pmtt) REVERT: F 76 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7539 (mtpt) REVERT: F 81 ASP cc_start: 0.8326 (t0) cc_final: 0.7996 (t0) REVERT: F 123 LYS cc_start: 0.8857 (tppt) cc_final: 0.8639 (tppt) REVERT: J 500 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8034 (pt0) outliers start: 86 outliers final: 51 residues processed: 657 average time/residue: 1.2700 time to fit residues: 941.2554 Evaluate side-chains 650 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 591 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 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 I residue 474 THR Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain N residue 72 ASN 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 73 CYS Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain V residue 483 ILE Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain 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 101 ASN 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 F residue 76 LYS Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 500 GLU Chi-restraints excluded: chain K residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 182 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 219 optimal weight: 0.0670 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 68 GLN ** 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** N 58 GLN N 101 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 74 HIS R 101 ASN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN S 110 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN E 103 GLN E 110 GLN G 74 HIS G 101 ASN ** 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 Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.125257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099958 restraints weight = 49963.471| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.61 r_work: 0.3374 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20223 Z= 0.149 Angle : 0.748 12.280 27351 Z= 0.370 Chirality : 0.047 0.232 2905 Planarity : 0.004 0.088 3638 Dihedral : 4.766 57.022 2703 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.57 % Allowed : 35.33 % Favored : 61.10 % 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: 1.51 (0.19), residues: 2415 helix: 2.21 (0.20), residues: 632 sheet: 0.16 (0.18), residues: 738 loop : 1.11 (0.23), residues: 1045 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 0.018 0.002 PHE Q 112 TYR 0.022 0.001 TYR O 125 ARG 0.023 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 909) hydrogen bonds : angle 4.93956 ( 2565) covalent geometry : bond 0.00350 (20223) covalent geometry : angle 0.74844 (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 680 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 603 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8506 (tp30) cc_final: 0.7886 (tp30) REVERT: A 87 ASN cc_start: 0.9076 (m-40) cc_final: 0.8834 (m110) REVERT: A 88 ASP cc_start: 0.8373 (t0) cc_final: 0.8048 (t0) REVERT: A 134 GLN cc_start: 0.7575 (tt0) cc_final: 0.7321 (tt0) REVERT: C 14 GLU cc_start: 0.7495 (tp30) cc_final: 0.7104 (tp30) REVERT: C 36 LYS cc_start: 0.8894 (mptt) cc_final: 0.8633 (mppt) REVERT: C 63 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8525 (tmm-80) REVERT: C 101 ASN cc_start: 0.8923 (m-40) cc_final: 0.8567 (m110) REVERT: C 103 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8752 (mm-40) REVERT: C 109 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: D 13 ARG cc_start: 0.8890 (mmt90) cc_final: 0.8474 (mmm-85) REVERT: D 14 GLU cc_start: 0.9097 (tp30) cc_final: 0.8742 (tp30) REVERT: D 17 ARG cc_start: 0.8877 (ttp80) cc_final: 0.8554 (ttp80) REVERT: D 29 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8190 (mtp) REVERT: B 50 LYS cc_start: 0.8840 (pttt) cc_final: 0.8591 (mmmt) REVERT: B 66 MET cc_start: 0.8776 (mmm) cc_final: 0.8478 (mmm) REVERT: L 484 GLU cc_start: 0.8931 (mp0) cc_final: 0.8563 (mp0) REVERT: I 500 GLU cc_start: 0.8068 (tt0) cc_final: 0.7846 (tt0) REVERT: I 504 LEU cc_start: 0.9013 (mm) cc_final: 0.8786 (mp) REVERT: P 5 LYS cc_start: 0.9269 (mtpp) cc_final: 0.8949 (tttp) REVERT: P 68 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: P 81 ASP cc_start: 0.7998 (m-30) cc_final: 0.7652 (t0) REVERT: P 87 ASN cc_start: 0.9370 (m-40) cc_final: 0.9061 (m-40) REVERT: P 103 GLN cc_start: 0.8873 (mm110) cc_final: 0.8628 (mt0) REVERT: N 14 GLU cc_start: 0.7306 (tp30) cc_final: 0.6879 (tp30) REVERT: N 36 LYS cc_start: 0.8761 (tptp) cc_final: 0.8335 (mppt) REVERT: N 63 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8429 (ttm-80) REVERT: N 74 HIS cc_start: 0.7843 (m90) cc_final: 0.7559 (m-70) REVERT: N 88 ASP cc_start: 0.8340 (t0) cc_final: 0.8054 (t0) REVERT: N 103 GLN cc_start: 0.9043 (mm110) cc_final: 0.8642 (mp10) REVERT: M 29 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (mtt) REVERT: M 32 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8617 (mmm-85) REVERT: M 68 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7736 (pt0) REVERT: M 70 PHE cc_start: 0.8817 (m-80) cc_final: 0.8568 (m-80) REVERT: M 88 ASP cc_start: 0.9170 (m-30) cc_final: 0.8772 (t0) REVERT: O 50 LYS cc_start: 0.8712 (pptt) cc_final: 0.8272 (pmtt) REVERT: O 66 MET cc_start: 0.8750 (mmm) cc_final: 0.8443 (mmm) REVERT: U 500 GLU cc_start: 0.8541 (tt0) cc_final: 0.8053 (tt0) REVERT: T 5 LYS cc_start: 0.8992 (mtpm) cc_final: 0.8671 (ttmt) REVERT: T 14 GLU cc_start: 0.8652 (tp30) cc_final: 0.8061 (tp30) REVERT: T 76 LYS cc_start: 0.8479 (tptm) cc_final: 0.8179 (tptt) REVERT: T 87 ASN cc_start: 0.9085 (m-40) cc_final: 0.8767 (m-40) REVERT: T 88 ASP cc_start: 0.8558 (t0) cc_final: 0.8143 (t0) REVERT: R 1 MET cc_start: 0.6604 (ptm) cc_final: 0.6401 (ptm) REVERT: R 14 GLU cc_start: 0.7363 (tp30) cc_final: 0.6955 (tp30) REVERT: R 25 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8380 (mm110) REVERT: R 29 MET cc_start: 0.8435 (mmp) cc_final: 0.8095 (mtp) REVERT: R 36 LYS cc_start: 0.8994 (mptt) cc_final: 0.8543 (mppt) REVERT: R 48 ASN cc_start: 0.8703 (t0) cc_final: 0.8369 (t0) REVERT: R 88 ASP cc_start: 0.8383 (t0) cc_final: 0.8055 (t0) REVERT: Q 13 ARG cc_start: 0.8768 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: Q 29 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (mtt) REVERT: Q 68 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7796 (tp40) REVERT: Q 71 THR cc_start: 0.8774 (t) cc_final: 0.8228 (p) REVERT: Q 136 GLU cc_start: 0.8896 (pt0) cc_final: 0.8402 (pp20) REVERT: S 14 GLU cc_start: 0.8241 (tp30) cc_final: 0.7809 (tp30) REVERT: S 46 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6319 (p0) REVERT: S 50 LYS cc_start: 0.8841 (pptt) cc_final: 0.8308 (pmtt) REVERT: S 66 MET cc_start: 0.8799 (mmm) cc_final: 0.8520 (mmm) REVERT: S 109 MET cc_start: 0.7868 (mmt) cc_final: 0.7530 (mmt) REVERT: X 500 GLU cc_start: 0.8469 (tt0) cc_final: 0.8167 (tt0) REVERT: X 504 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8042 (mp) REVERT: W 500 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8190 (mt-10) REVERT: E 5 LYS cc_start: 0.9120 (mtpm) cc_final: 0.8798 (tttp) REVERT: E 14 GLU cc_start: 0.8517 (tp30) cc_final: 0.8087 (tp30) REVERT: E 68 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7947 (mm-40) REVERT: E 76 LYS cc_start: 0.8580 (tppp) cc_final: 0.8193 (tptt) REVERT: E 103 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: G 3 MET cc_start: 0.7546 (tpp) cc_final: 0.7113 (tpp) REVERT: G 14 GLU cc_start: 0.7319 (tp30) cc_final: 0.6917 (tp30) REVERT: G 37 ASN cc_start: 0.8478 (t0) cc_final: 0.8219 (t0) REVERT: G 88 ASP cc_start: 0.8224 (t0) cc_final: 0.7865 (t0) REVERT: G 103 GLN cc_start: 0.9107 (mm110) cc_final: 0.8669 (mp10) REVERT: G 117 GLU cc_start: 0.9103 (tt0) cc_final: 0.8871 (tt0) REVERT: H 32 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8926 (mmm-85) REVERT: H 71 THR cc_start: 0.9061 (t) cc_final: 0.8374 (p) REVERT: H 88 ASP cc_start: 0.9186 (m-30) cc_final: 0.8610 (t0) REVERT: H 117 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8233 (mt-10) REVERT: F 76 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7524 (mtpt) REVERT: F 81 ASP cc_start: 0.8325 (t0) cc_final: 0.7967 (t0) REVERT: F 123 LYS cc_start: 0.8861 (tppt) cc_final: 0.8642 (tppt) REVERT: J 500 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7989 (pt0) outliers start: 77 outliers final: 49 residues processed: 641 average time/residue: 1.2505 time to fit residues: 904.7049 Evaluate side-chains 647 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 588 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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 97 LEU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 29 MET Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 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 L residue 483 ILE 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 P residue 99 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain M residue 18 GLN 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 73 CYS Chi-restraints excluded: chain M residue 90 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 53 ASP Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 504 LEU Chi-restraints excluded: chain W residue 474 THR Chi-restraints excluded: chain W residue 485 SER 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 39 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 59 LYS 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 500 GLU Chi-restraints excluded: chain K residue 485 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 110 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 37 ASN C 68 GLN C 72 ASN 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 ASN N 101 ASN ** N 134 GLN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 110 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 ASN R 101 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN G 74 HIS ** 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 Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099064 restraints weight = 54845.764| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.79 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.483 20223 Z= 0.310 Angle : 1.032 59.199 27351 Z= 0.578 Chirality : 0.049 0.551 2905 Planarity : 0.005 0.127 3638 Dihedral : 4.793 57.016 2703 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.52 % Allowed : 35.42 % Favored : 61.06 % Cbeta Deviations : 0.09 % 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: 1.49 (0.18), residues: 2415 helix: 2.18 (0.20), residues: 632 sheet: 0.16 (0.18), residues: 738 loop : 1.08 (0.23), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 509 HIS 0.005 0.001 HIS S 79 PHE 0.019 0.002 PHE Q 112 TYR 0.021 0.001 TYR N 40 ARG 0.016 0.001 ARG M 17 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 909) hydrogen bonds : angle 4.93818 ( 2565) covalent geometry : bond 0.00712 (20223) covalent geometry : angle 1.03202 (27351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18822.62 seconds wall clock time: 320 minutes 19.53 seconds (19219.53 seconds total)