Starting phenix.real_space_refine on Thu Jan 16 17:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i1x_0326/01_2025/6i1x_0326_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i1x_0326/01_2025/6i1x_0326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6i1x_0326/01_2025/6i1x_0326.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i1x_0326/01_2025/6i1x_0326.map" model { file = "/net/cci-nas-00/data/ceres_data/6i1x_0326/01_2025/6i1x_0326_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i1x_0326/01_2025/6i1x_0326_neut.cif" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.009 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 150 5.16 5 C 34155 2.51 5 N 9675 2.21 5 O 10935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54915 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "D" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "E" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "F" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "H" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "I" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "J" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "K" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "L" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "M" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "N" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "O" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Time building chain proxies: 22.17, per 1000 atoms: 0.40 Number of scatterers: 54915 At special positions: 0 Unit cell: (158.51, 157.3, 182.71, 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 150 16.00 O 10935 8.00 N 9675 7.00 C 34155 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 5.6 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13290 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 0 sheets defined 32.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 removed outlier: 3.723A pdb=" N GLU A 114 " --> pdb=" O SER A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.888A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.596A pdb=" N GLN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.852A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU B 114 " --> pdb=" O SER B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.910A pdb=" N GLY B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 220 through 235 removed outlier: 3.589A pdb=" N GLN B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.851A pdb=" N GLU B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 578 through 607 removed outlier: 3.658A pdb=" N GLY B 583 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 588 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 removed outlier: 3.736A pdb=" N GLU C 114 " --> pdb=" O SER C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.896A pdb=" N GLY C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.590A pdb=" N GLN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.847A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 323 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY C 583 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 588 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU D 114 " --> pdb=" O SER D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.892A pdb=" N GLY D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.837A pdb=" N GLU D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 383 through 390 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY D 583 " --> pdb=" O ASN D 579 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 588 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 removed outlier: 3.725A pdb=" N GLU E 114 " --> pdb=" O SER E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 115 through 124 Processing helix chain 'E' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.625A pdb=" N GLN E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.805A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 323 Processing helix chain 'E' and resid 366 through 377 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 543 through 547 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 578 through 607 removed outlier: 3.644A pdb=" N GLY E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 588 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR E 605 " --> pdb=" O ALA E 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU F 114 " --> pdb=" O SER F 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.632A pdb=" N GLN F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.822A pdb=" N GLU F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL F 264 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 323 Processing helix chain 'F' and resid 366 through 377 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 549 through 554 Processing helix chain 'F' and resid 578 through 607 removed outlier: 3.665A pdb=" N GLY F 583 " --> pdb=" O ASN F 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 588 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 removed outlier: 3.704A pdb=" N GLU G 114 " --> pdb=" O SER G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 115 through 124 Processing helix chain 'G' and resid 145 through 163 removed outlier: 3.878A pdb=" N GLY G 163 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 220 through 234 removed outlier: 3.644A pdb=" N GLN G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.804A pdb=" N GLU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 263 " --> pdb=" O GLU G 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 323 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 383 through 390 Processing helix chain 'G' and resid 543 through 547 Processing helix chain 'G' and resid 549 through 554 Processing helix chain 'G' and resid 578 through 607 removed outlier: 3.660A pdb=" N GLY G 583 " --> pdb=" O ASN G 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 588 " --> pdb=" O ILE G 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU H 114 " --> pdb=" O SER H 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 114' Processing helix chain 'H' and resid 115 through 124 Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.907A pdb=" N GLY H 163 " --> pdb=" O VAL H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 220 through 234 removed outlier: 3.623A pdb=" N GLN H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 263 " --> pdb=" O GLU H 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 323 Processing helix chain 'H' and resid 366 through 377 Processing helix chain 'H' and resid 383 through 390 Processing helix chain 'H' and resid 543 through 547 Processing helix chain 'H' and resid 549 through 554 Processing helix chain 'H' and resid 578 through 607 removed outlier: 3.662A pdb=" N GLY H 583 " --> pdb=" O ASN H 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 588 " --> pdb=" O ILE H 584 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 removed outlier: 3.758A pdb=" N GLU I 114 " --> pdb=" O SER I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 114' Processing helix chain 'I' and resid 115 through 124 Processing helix chain 'I' and resid 145 through 163 removed outlier: 3.863A pdb=" N GLY I 163 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 220 through 235 removed outlier: 3.637A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.833A pdb=" N GLU I 259 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY I 263 " --> pdb=" O GLU I 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 323 Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.512A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 390 Processing helix chain 'I' and resid 543 through 547 Processing helix chain 'I' and resid 549 through 554 Processing helix chain 'I' and resid 578 through 607 removed outlier: 3.673A pdb=" N GLY I 583 " --> pdb=" O ASN I 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 588 " --> pdb=" O ILE I 584 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR I 605 " --> pdb=" O ALA I 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 removed outlier: 3.744A pdb=" N GLU J 114 " --> pdb=" O SER J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 115 through 124 Processing helix chain 'J' and resid 145 through 163 removed outlier: 3.897A pdb=" N GLY J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 220 through 235 removed outlier: 3.587A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU J 259 " --> pdb=" O LYS J 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL J 264 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 323 Processing helix chain 'J' and resid 366 through 377 Processing helix chain 'J' and resid 383 through 390 Processing helix chain 'J' and resid 543 through 547 Processing helix chain 'J' and resid 549 through 554 Processing helix chain 'J' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY J 583 " --> pdb=" O ASN J 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 588 " --> pdb=" O ILE J 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR J 605 " --> pdb=" O ALA J 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU K 114 " --> pdb=" O SER K 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 111 through 114' Processing helix chain 'K' and resid 115 through 124 Processing helix chain 'K' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY K 163 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU K 259 " --> pdb=" O LYS K 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 323 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 383 through 390 Processing helix chain 'K' and resid 543 through 547 Processing helix chain 'K' and resid 549 through 554 Processing helix chain 'K' and resid 578 through 607 removed outlier: 3.656A pdb=" N GLY K 583 " --> pdb=" O ASN K 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS K 588 " --> pdb=" O ILE K 584 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR K 605 " --> pdb=" O ALA K 601 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU L 114 " --> pdb=" O SER L 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 111 through 114' Processing helix chain 'L' and resid 115 through 124 Processing helix chain 'L' and resid 145 through 163 removed outlier: 3.901A pdb=" N GLY L 163 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 199 through 203 Processing helix chain 'L' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU L 259 " --> pdb=" O LYS L 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 323 Processing helix chain 'L' and resid 366 through 377 Processing helix chain 'L' and resid 383 through 390 Processing helix chain 'L' and resid 543 through 547 Processing helix chain 'L' and resid 549 through 554 Processing helix chain 'L' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY L 583 " --> pdb=" O ASN L 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS L 588 " --> pdb=" O ILE L 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR L 605 " --> pdb=" O ALA L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 removed outlier: 3.735A pdb=" N GLU M 114 " --> pdb=" O SER M 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 111 through 114' Processing helix chain 'M' and resid 115 through 124 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.903A pdb=" N GLY M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 199 through 203 Processing helix chain 'M' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 removed outlier: 3.842A pdb=" N GLU M 259 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY M 263 " --> pdb=" O GLU M 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 323 Processing helix chain 'M' and resid 366 through 377 Processing helix chain 'M' and resid 383 through 390 Processing helix chain 'M' and resid 543 through 547 Processing helix chain 'M' and resid 549 through 554 Processing helix chain 'M' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY M 583 " --> pdb=" O ASN M 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS M 588 " --> pdb=" O ILE M 584 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR M 605 " --> pdb=" O ALA M 601 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 removed outlier: 3.722A pdb=" N GLU N 114 " --> pdb=" O SER N 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 111 through 114' Processing helix chain 'N' and resid 115 through 124 Processing helix chain 'N' and resid 145 through 163 removed outlier: 3.895A pdb=" N GLY N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 220 through 234 removed outlier: 3.600A pdb=" N GLN N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU N 259 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 323 Processing helix chain 'N' and resid 366 through 377 Processing helix chain 'N' and resid 383 through 390 Processing helix chain 'N' and resid 543 through 547 Processing helix chain 'N' and resid 549 through 554 Processing helix chain 'N' and resid 578 through 607 removed outlier: 3.657A pdb=" N GLY N 583 " --> pdb=" O ASN N 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS N 588 " --> pdb=" O ILE N 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR N 605 " --> pdb=" O ALA N 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 removed outlier: 3.724A pdb=" N GLU O 114 " --> pdb=" O SER O 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 111 through 114' Processing helix chain 'O' and resid 115 through 124 Processing helix chain 'O' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 199 through 203 Processing helix chain 'O' and resid 220 through 234 removed outlier: 3.598A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU O 259 " --> pdb=" O LYS O 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 323 Processing helix chain 'O' and resid 366 through 377 Processing helix chain 'O' and resid 383 through 390 Processing helix chain 'O' and resid 543 through 547 Processing helix chain 'O' and resid 549 through 554 Processing helix chain 'O' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY O 583 " --> pdb=" O ASN O 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS O 588 " --> pdb=" O ILE O 584 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR O 605 " --> pdb=" O ALA O 601 " (cutoff:3.500A) 1459 hydrogen bonds defined for protein. 4062 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: 11.12 Time building geometry restraints manager: 12.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11082 1.32 - 1.45: 11247 1.45 - 1.58: 32856 1.58 - 1.70: 0 1.70 - 1.83: 300 Bond restraints: 55485 Sorted by residual: bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.520 1.545 -0.026 4.80e-03 4.34e+04 2.89e+01 bond pdb=" CA TYR G 174 " pdb=" C TYR G 174 " ideal model delta sigma weight residual 1.520 1.544 -0.025 4.80e-03 4.34e+04 2.65e+01 bond pdb=" CA TYR N 174 " pdb=" C TYR N 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.60e+01 bond pdb=" CA TYR K 174 " pdb=" C TYR K 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 ... (remaining 55480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 53796 1.88 - 3.76: 18358 3.76 - 5.64: 2776 5.64 - 7.52: 246 7.52 - 9.40: 79 Bond angle restraints: 75255 Sorted by residual: angle pdb=" N PRO I 609 " pdb=" CA PRO I 609 " pdb=" CB PRO I 609 " ideal model delta sigma weight residual 103.25 94.24 9.01 1.05e+00 9.07e-01 7.36e+01 angle pdb=" N PRO D 609 " pdb=" CA PRO D 609 " pdb=" CB PRO D 609 " ideal model delta sigma weight residual 103.25 94.43 8.82 1.05e+00 9.07e-01 7.06e+01 angle pdb=" N PRO H 609 " pdb=" CA PRO H 609 " pdb=" CB PRO H 609 " ideal model delta sigma weight residual 103.25 94.45 8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO B 609 " pdb=" CA PRO B 609 " pdb=" CB PRO B 609 " ideal model delta sigma weight residual 103.25 94.49 8.76 1.05e+00 9.07e-01 6.96e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" CB PRO C 609 " ideal model delta sigma weight residual 103.25 94.50 8.75 1.05e+00 9.07e-01 6.94e+01 ... (remaining 75250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 30582 18.10 - 36.19: 2588 36.19 - 54.29: 609 54.29 - 72.39: 121 72.39 - 90.49: 30 Dihedral angle restraints: 33930 sinusoidal: 13230 harmonic: 20700 Sorted by residual: dihedral pdb=" CA LYS I 189 " pdb=" C LYS I 189 " pdb=" N ASP I 190 " pdb=" CA ASP I 190 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS H 189 " pdb=" C LYS H 189 " pdb=" N ASP H 190 " pdb=" CA ASP H 190 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA LYS G 189 " pdb=" C LYS G 189 " pdb=" N ASP G 190 " pdb=" CA ASP G 190 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 33927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3853 0.061 - 0.123: 3239 0.123 - 0.184: 1572 0.184 - 0.245: 391 0.245 - 0.306: 65 Chirality restraints: 9120 Sorted by residual: chirality pdb=" CA LYS E 250 " pdb=" N LYS E 250 " pdb=" C LYS E 250 " pdb=" CB LYS E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS F 250 " pdb=" N LYS F 250 " pdb=" C LYS F 250 " pdb=" CB LYS F 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS L 250 " pdb=" N LYS L 250 " pdb=" C LYS L 250 " pdb=" CB LYS L 250 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 9117 not shown) Planarity restraints: 9855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 613 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C VAL F 613 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL F 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 613 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL B 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 613 " 0.017 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C VAL H 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU H 614 " 0.022 2.00e-02 2.50e+03 ... (remaining 9852 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.63: 5 1.63 - 2.45: 291 2.45 - 3.27: 60982 3.27 - 4.08: 141562 4.08 - 4.90: 250522 Warning: very small nonbonded interaction distances. Nonbonded interactions: 453362 Sorted by model distance: nonbonded pdb=" CB VAL H 139 " pdb=" O ALA I 162 " model vdw 0.818 3.470 nonbonded pdb=" CG2 VAL H 139 " pdb=" O ALA I 162 " model vdw 1.091 2.768 nonbonded pdb=" ND2 ASN I 138 " pdb=" O THR J 198 " model vdw 1.323 3.120 nonbonded pdb=" CA VAL H 139 " pdb=" O ALA I 162 " model vdw 1.467 3.470 nonbonded pdb=" NE2 GLN E 328 " pdb=" O LEU F 517 " model vdw 1.591 3.120 ... (remaining 453357 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: 0.38 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.060 Extract box with map and model: 1.530 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 81.260 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.280 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3237 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 : 0.013 0.061 55485 Z= 0.838 Angle : 1.810 9.397 75255 Z= 1.296 Chirality : 0.098 0.306 9120 Planarity : 0.008 0.072 9855 Dihedral : 14.937 90.487 20640 Min Nonbonded Distance : 0.818 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.50 % Favored : 90.61 % Rotamer: Outliers : 4.35 % Allowed : 8.17 % Favored : 87.48 % Cbeta Deviations : 0.51 % 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: -3.51 (0.08), residues: 7200 helix: -2.95 (0.08), residues: 1965 sheet: -1.10 (0.10), residues: 2175 loop : -2.72 (0.08), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP I 350 HIS 0.006 0.003 HIS H 133 PHE 0.035 0.007 PHE E 247 TYR 0.039 0.007 TYR H 134 ARG 0.009 0.001 ARG F 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 263 poor density : 1541 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.5898 (t) cc_final: 0.4828 (t) REVERT: A 211 ARG cc_start: 0.4395 (mtt180) cc_final: 0.4192 (ttt180) REVERT: A 229 GLN cc_start: 0.7222 (mt0) cc_final: 0.7018 (mm-40) REVERT: A 255 LYS cc_start: 0.6764 (tttt) cc_final: 0.6536 (mmtt) REVERT: A 259 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5626 (mt-10) REVERT: A 298 GLU cc_start: 0.6169 (tt0) cc_final: 0.5812 (pm20) REVERT: A 312 MET cc_start: 0.7262 (tpp) cc_final: 0.6962 (mmm) REVERT: A 345 ASN cc_start: 0.6678 (p0) cc_final: 0.6193 (p0) REVERT: A 407 MET cc_start: 0.3897 (ttp) cc_final: 0.3218 (tmm) REVERT: A 413 SER cc_start: 0.5500 (m) cc_final: 0.5171 (t) REVERT: A 433 GLU cc_start: 0.6624 (pt0) cc_final: 0.6287 (mt-10) REVERT: A 478 GLU cc_start: 0.7534 (tp30) cc_final: 0.7005 (pp20) REVERT: A 487 GLU cc_start: 0.4338 (tt0) cc_final: 0.4085 (tp30) REVERT: A 534 THR cc_start: 0.7041 (m) cc_final: 0.6302 (m) REVERT: A 550 LEU cc_start: 0.7533 (mt) cc_final: 0.7132 (tp) REVERT: A 553 LEU cc_start: 0.7238 (mt) cc_final: 0.6916 (mt) REVERT: A 558 SER cc_start: 0.3396 (t) cc_final: 0.2744 (m) REVERT: A 560 ASN cc_start: 0.6903 (t0) cc_final: 0.6640 (t0) REVERT: A 591 LEU cc_start: 0.8430 (tp) cc_final: 0.8174 (tp) REVERT: A 602 GLN cc_start: 0.5736 (mt0) cc_final: 0.5511 (tp40) REVERT: B 167 VAL cc_start: 0.6045 (t) cc_final: 0.5403 (t) REVERT: B 174 TYR cc_start: 0.4200 (m-80) cc_final: 0.3920 (m-80) REVERT: B 229 GLN cc_start: 0.6882 (mt0) cc_final: 0.6565 (mm-40) REVERT: B 312 MET cc_start: 0.7779 (tpp) cc_final: 0.7559 (mmm) REVERT: B 345 ASN cc_start: 0.6405 (p0) cc_final: 0.6085 (t0) REVERT: B 359 GLN cc_start: 0.6386 (tt0) cc_final: 0.5970 (tp40) REVERT: B 413 SER cc_start: 0.5064 (m) cc_final: 0.4641 (t) REVERT: B 433 GLU cc_start: 0.6281 (pt0) cc_final: 0.5772 (mp0) REVERT: B 461 ILE cc_start: 0.2494 (OUTLIER) cc_final: 0.2009 (pt) REVERT: B 478 GLU cc_start: 0.7408 (tp30) cc_final: 0.6958 (pp20) REVERT: B 535 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7529 (tttp) REVERT: B 550 LEU cc_start: 0.7398 (mt) cc_final: 0.6814 (tt) REVERT: B 562 SER cc_start: 0.6415 (m) cc_final: 0.6054 (t) REVERT: B 579 ASN cc_start: 0.7270 (m-40) cc_final: 0.6862 (p0) REVERT: B 602 GLN cc_start: 0.7041 (mt0) cc_final: 0.6598 (tp40) REVERT: C 167 VAL cc_start: 0.6930 (t) cc_final: 0.6472 (t) REVERT: C 229 GLN cc_start: 0.7270 (mt0) cc_final: 0.6895 (mm-40) REVERT: C 312 MET cc_start: 0.7687 (tpp) cc_final: 0.7454 (mmm) REVERT: C 325 ARG cc_start: 0.6063 (ttt180) cc_final: 0.5832 (ttm110) REVERT: C 345 ASN cc_start: 0.6445 (p0) cc_final: 0.5918 (t0) REVERT: C 413 SER cc_start: 0.5241 (m) cc_final: 0.4691 (t) REVERT: C 429 MET cc_start: 0.3990 (mmm) cc_final: 0.2918 (mmm) REVERT: C 430 ASP cc_start: 0.3511 (p0) cc_final: 0.2516 (p0) REVERT: C 433 GLU cc_start: 0.6744 (pt0) cc_final: 0.6390 (mt-10) REVERT: C 461 ILE cc_start: 0.2834 (OUTLIER) cc_final: 0.2043 (pt) REVERT: C 463 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.2888 (mtp85) REVERT: C 503 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4262 (mt) REVERT: C 535 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7400 (tttp) REVERT: C 550 LEU cc_start: 0.7228 (mt) cc_final: 0.6808 (tt) REVERT: C 567 MET cc_start: 0.5010 (mmm) cc_final: 0.4806 (mmt) REVERT: C 579 ASN cc_start: 0.7525 (m-40) cc_final: 0.7051 (p0) REVERT: C 591 LEU cc_start: 0.8483 (tp) cc_final: 0.8259 (tp) REVERT: C 602 GLN cc_start: 0.7049 (mt0) cc_final: 0.6784 (tp40) REVERT: D 215 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7461 (p) REVERT: D 227 ILE cc_start: 0.7450 (mt) cc_final: 0.7203 (tp) REVERT: D 229 GLN cc_start: 0.7229 (mt0) cc_final: 0.7000 (mm-40) REVERT: D 259 GLU cc_start: 0.6188 (mm-30) cc_final: 0.5848 (mt-10) REVERT: D 312 MET cc_start: 0.7642 (tpp) cc_final: 0.7439 (mmm) REVERT: D 325 ARG cc_start: 0.6569 (ttt180) cc_final: 0.6263 (ttm170) REVERT: D 345 ASN cc_start: 0.6464 (p0) cc_final: 0.6211 (t0) REVERT: D 433 GLU cc_start: 0.6726 (pt0) cc_final: 0.6417 (mt-10) REVERT: D 463 ARG cc_start: 0.2642 (OUTLIER) cc_final: 0.2344 (mtp85) REVERT: D 475 GLN cc_start: 0.4699 (tt0) cc_final: 0.4286 (tm-30) REVERT: D 535 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7352 (tttp) REVERT: D 550 LEU cc_start: 0.7339 (mt) cc_final: 0.6915 (tt) REVERT: D 562 SER cc_start: 0.6220 (m) cc_final: 0.5860 (t) REVERT: D 579 ASN cc_start: 0.7226 (m-40) cc_final: 0.6804 (p0) REVERT: D 602 GLN cc_start: 0.6813 (mt0) cc_final: 0.6566 (tp40) REVERT: E 190 ASP cc_start: -0.2286 (OUTLIER) cc_final: -0.3142 (m-30) REVERT: E 227 ILE cc_start: 0.7592 (mt) cc_final: 0.7298 (mm) REVERT: E 238 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4930 (tp) REVERT: E 246 VAL cc_start: 0.7019 (t) cc_final: 0.6588 (p) REVERT: E 345 ASN cc_start: 0.6552 (p0) cc_final: 0.6330 (p0) REVERT: E 413 SER cc_start: 0.5873 (m) cc_final: 0.5558 (t) REVERT: E 433 GLU cc_start: 0.6246 (pt0) cc_final: 0.6013 (mt-10) REVERT: E 461 ILE cc_start: 0.3244 (OUTLIER) cc_final: 0.2368 (pt) REVERT: E 478 GLU cc_start: 0.7186 (tp30) cc_final: 0.6794 (pp20) REVERT: E 503 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4020 (mt) REVERT: E 534 THR cc_start: 0.7699 (m) cc_final: 0.7352 (m) REVERT: E 535 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7327 (tttp) REVERT: E 579 ASN cc_start: 0.7110 (m-40) cc_final: 0.6801 (p0) REVERT: F 160 ASP cc_start: 0.6044 (t70) cc_final: 0.5828 (m-30) REVERT: F 174 TYR cc_start: 0.4414 (m-80) cc_final: 0.4160 (m-80) REVERT: F 215 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6173 (p) REVERT: F 232 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8177 (ptm-80) REVERT: F 244 THR cc_start: 0.6402 (m) cc_final: 0.6109 (m) REVERT: F 312 MET cc_start: 0.6542 (tpp) cc_final: 0.5845 (mmm) REVERT: F 365 PRO cc_start: 0.8019 (Cg_endo) cc_final: 0.7673 (Cg_exo) REVERT: F 433 GLU cc_start: 0.6266 (pt0) cc_final: 0.5896 (mt-10) REVERT: F 461 ILE cc_start: 0.3277 (OUTLIER) cc_final: 0.2646 (pt) REVERT: F 463 ARG cc_start: 0.2380 (OUTLIER) cc_final: 0.1961 (mtp85) REVERT: F 503 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4551 (mt) REVERT: F 530 MET cc_start: 0.3772 (mtm) cc_final: 0.3548 (mtt) REVERT: F 535 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7331 (tttp) REVERT: F 553 LEU cc_start: 0.7386 (mt) cc_final: 0.7155 (mp) REVERT: G 160 ASP cc_start: 0.6146 (t70) cc_final: 0.5686 (m-30) REVERT: G 215 VAL cc_start: 0.6304 (OUTLIER) cc_final: 0.6000 (p) REVERT: G 232 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8234 (mtm110) REVERT: G 241 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: G 246 VAL cc_start: 0.6866 (t) cc_final: 0.6475 (p) REVERT: G 255 LYS cc_start: 0.6839 (tttt) cc_final: 0.6551 (tppt) REVERT: G 365 PRO cc_start: 0.7539 (Cg_endo) cc_final: 0.7238 (Cg_exo) REVERT: G 433 GLU cc_start: 0.6087 (pt0) cc_final: 0.5763 (mt-10) REVERT: G 461 ILE cc_start: 0.3359 (OUTLIER) cc_final: 0.3068 (pt) REVERT: G 463 ARG cc_start: 0.1653 (OUTLIER) cc_final: 0.1412 (mtp85) REVERT: G 535 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7561 (tttp) REVERT: G 550 LEU cc_start: 0.7057 (mt) cc_final: 0.6780 (mt) REVERT: G 562 SER cc_start: 0.6525 (m) cc_final: 0.6267 (t) REVERT: G 579 ASN cc_start: 0.6898 (m-40) cc_final: 0.6368 (p0) REVERT: G 591 LEU cc_start: 0.8086 (tp) cc_final: 0.7803 (tp) REVERT: H 167 VAL cc_start: 0.6822 (t) cc_final: 0.5424 (t) REVERT: H 215 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7363 (p) REVERT: H 227 ILE cc_start: 0.7517 (mt) cc_final: 0.7175 (mm) REVERT: H 230 MET cc_start: 0.7314 (mtp) cc_final: 0.7102 (tmm) REVERT: H 255 LYS cc_start: 0.6555 (tttt) cc_final: 0.6343 (tppt) REVERT: H 316 GLU cc_start: 0.7936 (tt0) cc_final: 0.7455 (tm-30) REVERT: H 325 ARG cc_start: 0.6595 (ttt180) cc_final: 0.6372 (ttt-90) REVERT: H 345 ASN cc_start: 0.7034 (p0) cc_final: 0.6742 (p0) REVERT: H 407 MET cc_start: 0.5008 (ttp) cc_final: 0.4681 (tmm) REVERT: H 413 SER cc_start: 0.5764 (m) cc_final: 0.5407 (p) REVERT: H 433 GLU cc_start: 0.6432 (pt0) cc_final: 0.6066 (mt-10) REVERT: H 461 ILE cc_start: 0.2519 (OUTLIER) cc_final: 0.1907 (pt) REVERT: H 509 THR cc_start: 0.4432 (p) cc_final: 0.4186 (p) REVERT: H 530 MET cc_start: 0.4488 (mtm) cc_final: 0.4226 (mtt) REVERT: H 535 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7358 (tttp) REVERT: H 550 LEU cc_start: 0.7448 (mt) cc_final: 0.7078 (tt) REVERT: H 562 SER cc_start: 0.6484 (m) cc_final: 0.6134 (t) REVERT: H 567 MET cc_start: 0.4725 (mmm) cc_final: 0.4348 (mmt) REVERT: H 579 ASN cc_start: 0.7262 (m-40) cc_final: 0.6751 (p0) REVERT: I 180 MET cc_start: 0.5274 (mmm) cc_final: 0.5024 (mmp) REVERT: I 183 LEU cc_start: 0.6531 (mt) cc_final: 0.6275 (mt) REVERT: I 249 LEU cc_start: 0.5364 (mt) cc_final: 0.4381 (mp) REVERT: I 298 GLU cc_start: 0.7114 (tt0) cc_final: 0.6774 (pt0) REVERT: I 345 ASN cc_start: 0.6918 (p0) cc_final: 0.6691 (t0) REVERT: I 433 GLU cc_start: 0.6445 (pt0) cc_final: 0.6127 (mt-10) REVERT: I 463 ARG cc_start: 0.2832 (OUTLIER) cc_final: 0.2521 (mmm160) REVERT: I 478 GLU cc_start: 0.7549 (tp30) cc_final: 0.7241 (pp20) REVERT: I 480 ASP cc_start: 0.5224 (OUTLIER) cc_final: 0.5010 (p0) REVERT: I 534 THR cc_start: 0.7569 (m) cc_final: 0.7336 (m) REVERT: I 562 SER cc_start: 0.6426 (m) cc_final: 0.6132 (t) REVERT: J 180 MET cc_start: 0.4405 (mmm) cc_final: 0.4187 (mmm) REVERT: J 229 GLN cc_start: 0.7156 (mt0) cc_final: 0.6785 (mm-40) REVERT: J 236 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7992 (mmm160) REVERT: J 259 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5404 (mt-10) REVERT: J 326 ARG cc_start: 0.4557 (mtm-85) cc_final: 0.4311 (mtm110) REVERT: J 345 ASN cc_start: 0.7023 (p0) cc_final: 0.6607 (t0) REVERT: J 413 SER cc_start: 0.5659 (m) cc_final: 0.5153 (t) REVERT: J 424 PRO cc_start: 0.7689 (Cg_endo) cc_final: 0.7414 (Cg_exo) REVERT: J 433 GLU cc_start: 0.6775 (pt0) cc_final: 0.6439 (mt-10) REVERT: J 461 ILE cc_start: 0.2793 (OUTLIER) cc_final: 0.2220 (pt) REVERT: J 463 ARG cc_start: 0.2679 (OUTLIER) cc_final: 0.2436 (mtp85) REVERT: J 478 GLU cc_start: 0.7706 (tp30) cc_final: 0.7266 (pp20) REVERT: J 503 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4320 (mt) REVERT: J 550 LEU cc_start: 0.7299 (mt) cc_final: 0.6907 (tt) REVERT: J 562 SER cc_start: 0.6789 (m) cc_final: 0.6300 (t) REVERT: J 579 ASN cc_start: 0.7080 (m-40) cc_final: 0.6569 (p0) REVERT: J 602 GLN cc_start: 0.6679 (mt0) cc_final: 0.6398 (tp40) REVERT: K 168 ASP cc_start: 0.5282 (m-30) cc_final: 0.5066 (p0) REVERT: K 211 ARG cc_start: 0.5337 (mtt180) cc_final: 0.5095 (mtp85) REVERT: K 227 ILE cc_start: 0.7272 (mt) cc_final: 0.6895 (mm) REVERT: K 259 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5883 (mt-10) REVERT: K 312 MET cc_start: 0.7296 (tpp) cc_final: 0.6958 (mmm) REVERT: K 316 GLU cc_start: 0.8078 (tt0) cc_final: 0.7621 (tm-30) REVERT: K 430 ASP cc_start: 0.3201 (p0) cc_final: 0.2840 (p0) REVERT: K 433 GLU cc_start: 0.6683 (pt0) cc_final: 0.6419 (mt-10) REVERT: K 461 ILE cc_start: 0.2511 (OUTLIER) cc_final: 0.2010 (pt) REVERT: K 463 ARG cc_start: 0.2219 (OUTLIER) cc_final: 0.1808 (mtp85) REVERT: K 535 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7304 (tttm) REVERT: K 550 LEU cc_start: 0.7070 (mt) cc_final: 0.6692 (tt) REVERT: K 562 SER cc_start: 0.6848 (m) cc_final: 0.6424 (t) REVERT: K 567 MET cc_start: 0.5183 (mmm) cc_final: 0.4786 (mmm) REVERT: K 579 ASN cc_start: 0.7070 (m-40) cc_final: 0.6594 (p0) REVERT: L 174 TYR cc_start: 0.4523 (m-80) cc_final: 0.4297 (m-80) REVERT: L 229 GLN cc_start: 0.6929 (mt0) cc_final: 0.6610 (mm-40) REVERT: L 312 MET cc_start: 0.7488 (tpp) cc_final: 0.7225 (mmm) REVERT: L 345 ASN cc_start: 0.6745 (p0) cc_final: 0.6417 (t0) REVERT: L 359 GLN cc_start: 0.5251 (tt0) cc_final: 0.4977 (tp40) REVERT: L 413 SER cc_start: 0.5657 (m) cc_final: 0.5201 (t) REVERT: L 433 GLU cc_start: 0.6859 (pt0) cc_final: 0.6619 (mt-10) REVERT: L 461 ILE cc_start: 0.3046 (OUTLIER) cc_final: 0.2558 (pt) REVERT: L 463 ARG cc_start: 0.3109 (OUTLIER) cc_final: 0.2684 (mtp85) REVERT: L 478 GLU cc_start: 0.7772 (tp30) cc_final: 0.7333 (pp20) REVERT: L 534 THR cc_start: 0.7717 (m) cc_final: 0.7491 (m) REVERT: L 550 LEU cc_start: 0.7405 (mt) cc_final: 0.7025 (tt) REVERT: L 562 SER cc_start: 0.6657 (m) cc_final: 0.6301 (t) REVERT: L 579 ASN cc_start: 0.7154 (m-40) cc_final: 0.6776 (p0) REVERT: L 602 GLN cc_start: 0.6719 (mt0) cc_final: 0.6459 (tp40) REVERT: M 174 TYR cc_start: 0.4053 (m-80) cc_final: 0.3815 (m-80) REVERT: M 229 GLN cc_start: 0.6989 (mt0) cc_final: 0.6706 (mm-40) REVERT: M 325 ARG cc_start: 0.6651 (ttt180) cc_final: 0.6295 (tmt170) REVERT: M 345 ASN cc_start: 0.6900 (p0) cc_final: 0.6606 (t0) REVERT: M 359 GLN cc_start: 0.6013 (tt0) cc_final: 0.5623 (tp40) REVERT: M 413 SER cc_start: 0.5078 (m) cc_final: 0.4595 (t) REVERT: M 430 ASP cc_start: 0.3483 (p0) cc_final: 0.3174 (p0) REVERT: M 433 GLU cc_start: 0.6542 (pt0) cc_final: 0.6191 (mt-10) REVERT: M 461 ILE cc_start: 0.2910 (OUTLIER) cc_final: 0.2498 (pt) REVERT: M 463 ARG cc_start: 0.3010 (OUTLIER) cc_final: 0.2504 (mtp85) REVERT: M 475 GLN cc_start: 0.4524 (tt0) cc_final: 0.4267 (tm-30) REVERT: M 478 GLU cc_start: 0.7667 (tp30) cc_final: 0.7227 (pp20) REVERT: M 550 LEU cc_start: 0.7261 (mt) cc_final: 0.6846 (tt) REVERT: M 562 SER cc_start: 0.6636 (m) cc_final: 0.6264 (t) REVERT: M 579 ASN cc_start: 0.6789 (m-40) cc_final: 0.6272 (p0) REVERT: M 602 GLN cc_start: 0.6639 (mt0) cc_final: 0.6398 (tp40) REVERT: M 613 VAL cc_start: 0.4758 (p) cc_final: 0.4542 (t) REVERT: N 227 ILE cc_start: 0.7457 (mt) cc_final: 0.7206 (mm) REVERT: N 229 GLN cc_start: 0.6994 (mt0) cc_final: 0.6661 (mm-40) REVERT: N 259 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5528 (mt-10) REVERT: N 312 MET cc_start: 0.7468 (tpp) cc_final: 0.7090 (mmm) REVERT: N 345 ASN cc_start: 0.6314 (p0) cc_final: 0.5954 (t0) REVERT: N 359 GLN cc_start: 0.5930 (tt0) cc_final: 0.5524 (tp40) REVERT: N 407 MET cc_start: 0.4538 (ttp) cc_final: 0.4026 (tmm) REVERT: N 413 SER cc_start: 0.5514 (m) cc_final: 0.5042 (t) REVERT: N 424 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.7347 (Cg_exo) REVERT: N 433 GLU cc_start: 0.6114 (pt0) cc_final: 0.5806 (mt-10) REVERT: N 461 ILE cc_start: 0.2520 (OUTLIER) cc_final: 0.1944 (pt) REVERT: N 463 ARG cc_start: 0.2526 (OUTLIER) cc_final: 0.2231 (mtp85) REVERT: N 478 GLU cc_start: 0.7427 (tp30) cc_final: 0.7062 (pp20) REVERT: N 550 LEU cc_start: 0.7259 (mt) cc_final: 0.6838 (tt) REVERT: N 553 LEU cc_start: 0.7418 (mt) cc_final: 0.7206 (mt) REVERT: N 562 SER cc_start: 0.6543 (m) cc_final: 0.5930 (t) REVERT: N 579 ASN cc_start: 0.6941 (m-40) cc_final: 0.6415 (p0) REVERT: O 167 VAL cc_start: 0.6953 (t) cc_final: 0.6442 (t) REVERT: O 174 TYR cc_start: 0.4429 (m-80) cc_final: 0.4172 (m-80) REVERT: O 227 ILE cc_start: 0.7338 (mt) cc_final: 0.7130 (mm) REVERT: O 259 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5514 (mt-10) REVERT: O 298 GLU cc_start: 0.5711 (tt0) cc_final: 0.5471 (mt-10) REVERT: O 312 MET cc_start: 0.7650 (tpp) cc_final: 0.7320 (mmm) REVERT: O 413 SER cc_start: 0.5145 (m) cc_final: 0.4690 (t) REVERT: O 430 ASP cc_start: 0.3187 (p0) cc_final: 0.2769 (p0) REVERT: O 433 GLU cc_start: 0.6340 (pt0) cc_final: 0.6031 (mt-10) REVERT: O 463 ARG cc_start: 0.2364 (OUTLIER) cc_final: 0.2004 (mtp85) REVERT: O 478 GLU cc_start: 0.7568 (tp30) cc_final: 0.7188 (pp20) REVERT: O 534 THR cc_start: 0.7487 (m) cc_final: 0.7279 (m) REVERT: O 535 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7426 (tttp) REVERT: O 550 LEU cc_start: 0.7099 (mt) cc_final: 0.6578 (tt) REVERT: O 554 PHE cc_start: 0.7057 (m-80) cc_final: 0.6852 (m-80) REVERT: O 562 SER cc_start: 0.6826 (m) cc_final: 0.6391 (t) REVERT: O 579 ASN cc_start: 0.7201 (m-40) cc_final: 0.6753 (p0) REVERT: O 591 LEU cc_start: 0.8327 (tp) cc_final: 0.8062 (tp) REVERT: O 602 GLN cc_start: 0.7117 (mt0) cc_final: 0.6903 (tp-100) outliers start: 263 outliers final: 71 residues processed: 1752 average time/residue: 0.5551 time to fit residues: 1577.0600 Evaluate side-chains 932 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 827 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 463 ARG Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 492 SER Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 482 VAL Chi-restraints excluded: chain H residue 492 SER Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 482 VAL Chi-restraints excluded: chain I residue 492 SER Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 420 ILE Chi-restraints excluded: chain J residue 461 ILE Chi-restraints excluded: chain J residue 463 ARG Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 463 ARG Chi-restraints excluded: chain K residue 482 VAL Chi-restraints excluded: chain K residue 492 SER Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 482 VAL Chi-restraints excluded: chain L residue 492 SER Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 593 ARG Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 461 ILE Chi-restraints excluded: chain M residue 463 ARG Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 492 SER Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain N residue 190 ASP Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 420 ILE Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 463 ARG Chi-restraints excluded: chain N residue 482 VAL Chi-restraints excluded: chain N residue 492 SER Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 305 ILE Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 ARG Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 492 SER Chi-restraints excluded: chain O residue 503 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.9990 chunk 545 optimal weight: 2.9990 chunk 302 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 chunk 368 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 chunk 564 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 420 optimal weight: 5.9990 chunk 653 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 188 ASN A 328 GLN A 440 GLN A 496 GLN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 328 GLN B 440 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** B 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN C 496 GLN C 533 GLN ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 GLN D 440 GLN D 496 GLN E 186 ASN E 328 GLN E 440 GLN E 496 GLN E 533 GLN F 188 ASN F 328 GLN F 440 GLN F 475 GLN F 496 GLN G 138 ASN G 186 ASN G 233 GLN G 328 GLN G 440 GLN G 496 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 188 ASN H 328 GLN H 440 GLN H 496 GLN ** H 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 188 ASN I 328 GLN I 440 GLN I 496 GLN J 328 GLN J 440 GLN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN K 328 GLN K 394 ASN K 440 GLN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 GLN L 186 ASN L 188 ASN L 233 GLN L 328 GLN L 349 GLN L 440 GLN L 488 GLN L 496 GLN M 328 GLN M 349 GLN M 440 GLN M 496 GLN N 328 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 440 GLN N 496 GLN ** N 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 ASN O 188 ASN O 233 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 328 GLN O 345 ASN O 349 GLN O 440 GLN O 496 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.235905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.218561 restraints weight = 67921.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.219829 restraints weight = 114914.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.220762 restraints weight = 68385.274| |-----------------------------------------------------------------------------| r_work (final): 0.4811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.159 55485 Z= 0.263 Angle : 0.823 11.641 75255 Z= 0.422 Chirality : 0.051 0.243 9120 Planarity : 0.006 0.115 9855 Dihedral : 8.465 59.024 7990 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.07 % Favored : 96.54 % Rotamer: Outliers : 5.19 % Allowed : 14.19 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.22 (0.09), residues: 7200 helix: -0.80 (0.11), residues: 1950 sheet: -1.35 (0.09), residues: 2655 loop : -1.89 (0.10), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 350 HIS 0.008 0.003 HIS K 133 PHE 0.020 0.002 PHE I 393 TYR 0.034 0.003 TYR H 134 ARG 0.008 0.001 ARG M 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 314 poor density : 1013 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.1262 (ttt) cc_final: -0.1129 (mmt) REVERT: A 297 ASP cc_start: 0.7871 (t70) cc_final: 0.7606 (t70) REVERT: A 365 PRO cc_start: 0.5261 (Cg_endo) cc_final: 0.4991 (Cg_exo) REVERT: B 100 MET cc_start: 0.2745 (ttt) cc_final: -0.0083 (mmt) REVERT: B 342 ASP cc_start: 0.5290 (p0) cc_final: 0.4996 (p0) REVERT: D 172 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6303 (mm) REVERT: D 244 THR cc_start: 0.7110 (m) cc_final: 0.6860 (m) REVERT: D 463 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8109 (mtp85) REVERT: E 262 LYS cc_start: 0.7077 (mmmt) cc_final: 0.6819 (mmmt) REVERT: E 297 ASP cc_start: 0.6293 (t70) cc_final: 0.5991 (t0) REVERT: E 417 LYS cc_start: 0.7964 (tptt) cc_final: 0.7732 (ttpt) REVERT: G 445 GLN cc_start: 0.7775 (tp40) cc_final: 0.7548 (tm-30) REVERT: I 140 LEU cc_start: 0.5004 (OUTLIER) cc_final: 0.4803 (tt) REVERT: I 463 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8181 (mmt-90) REVERT: J 209 ASP cc_start: 0.6121 (t0) cc_final: 0.5820 (t0) REVERT: L 463 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8044 (mtp85) REVERT: L 529 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8069 (tt) REVERT: N 172 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6437 (mm) REVERT: O 172 LEU cc_start: 0.6689 (mt) cc_final: 0.6102 (mt) REVERT: O 297 ASP cc_start: 0.7468 (t0) cc_final: 0.7167 (t70) outliers start: 314 outliers final: 124 residues processed: 1259 average time/residue: 0.5012 time to fit residues: 1081.0412 Evaluate side-chains 809 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 678 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 465 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 559 ASN Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 559 ASN Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 190 ASP Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 530 MET Chi-restraints excluded: chain N residue 559 ASN Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 465 THR Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 559 ASN Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 118 optimal weight: 20.0000 chunk 371 optimal weight: 0.7980 chunk 564 optimal weight: 10.0000 chunk 622 optimal weight: 5.9990 chunk 568 optimal weight: 8.9990 chunk 582 optimal weight: 5.9990 chunk 437 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 522 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 GLN B 243 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN E 533 GLN ** F 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 533 GLN ** H 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 345 ASN L 533 GLN M 345 ASN M 533 GLN M 595 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 488 GLN O 533 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.226448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.213605 restraints weight = 68650.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.211811 restraints weight = 111821.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.209211 restraints weight = 68441.963| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 55485 Z= 0.300 Angle : 0.771 10.489 75255 Z= 0.393 Chirality : 0.049 0.201 9120 Planarity : 0.006 0.103 9855 Dihedral : 6.696 56.878 7829 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.40 % Favored : 95.18 % Rotamer: Outliers : 4.48 % Allowed : 18.63 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.09 (0.09), residues: 7200 helix: -0.25 (0.11), residues: 1950 sheet: -1.65 (0.09), residues: 2565 loop : -1.76 (0.11), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 350 HIS 0.005 0.002 HIS K 133 PHE 0.016 0.002 PHE J 592 TYR 0.039 0.002 TYR O 134 ARG 0.009 0.001 ARG J 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 796 time to evaluate : 4.529 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 141 LEU cc_start: 0.5827 (mp) cc_final: 0.4835 (tp) REVERT: A 365 PRO cc_start: 0.5281 (Cg_endo) cc_final: 0.4943 (Cg_exo) REVERT: B 243 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5642 (t0) REVERT: B 445 GLN cc_start: 0.7850 (tp40) cc_final: 0.7512 (tm-30) REVERT: D 172 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6551 (mm) REVERT: D 429 MET cc_start: 0.7455 (mmm) cc_final: 0.7221 (mmm) REVERT: E 297 ASP cc_start: 0.6456 (t70) cc_final: 0.6226 (t0) REVERT: E 336 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8256 (m) REVERT: E 421 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7470 (tt) REVERT: F 100 MET cc_start: 0.2307 (mmm) cc_final: 0.2070 (mmm) REVERT: F 421 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7979 (tt) REVERT: G 579 ASN cc_start: 0.6116 (t0) cc_final: 0.5607 (t0) REVERT: I 463 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7995 (mmt-90) REVERT: K 301 ASN cc_start: 0.6970 (t0) cc_final: 0.6756 (t0) REVERT: K 335 ILE cc_start: 0.8391 (mp) cc_final: 0.8176 (mp) REVERT: L 251 TYR cc_start: 0.6601 (m-80) cc_final: 0.5953 (m-80) REVERT: M 251 TYR cc_start: 0.6850 (m-80) cc_final: 0.6246 (m-80) REVERT: N 251 TYR cc_start: 0.6842 (m-80) cc_final: 0.5986 (m-80) REVERT: N 445 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7763 (mm-40) REVERT: O 167 VAL cc_start: 0.6842 (t) cc_final: 0.6504 (p) REVERT: O 251 TYR cc_start: 0.6967 (m-80) cc_final: 0.6260 (m-80) REVERT: O 469 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7435 (mtpp) outliers start: 271 outliers final: 170 residues processed: 990 average time/residue: 0.5033 time to fit residues: 854.2527 Evaluate side-chains 820 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 643 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 350 TRP Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 534 THR Chi-restraints excluded: chain J residue 550 LEU Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 550 LEU Chi-restraints excluded: chain K residue 557 THR Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 534 THR Chi-restraints excluded: chain L residue 557 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 534 THR Chi-restraints excluded: chain N residue 557 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 148 optimal weight: 1.9990 chunk 84 optimal weight: 0.0000 chunk 398 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 401 optimal weight: 1.9990 chunk 434 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 446 optimal weight: 10.0000 chunk 714 optimal weight: 20.0000 chunk 616 optimal weight: 20.0000 chunk 533 optimal weight: 20.0000 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 GLN B 243 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 GLN D 301 ASN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 188 ASN E 533 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 ASN ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN K 392 ASN ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN M 188 ASN M 233 GLN M 533 GLN N 394 ASN ** N 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN O 602 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.227054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.214179 restraints weight = 68394.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.212677 restraints weight = 111522.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.210153 restraints weight = 67579.331| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 55485 Z= 0.209 Angle : 0.699 12.230 75255 Z= 0.353 Chirality : 0.047 0.253 9120 Planarity : 0.005 0.091 9855 Dihedral : 5.962 56.236 7802 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.57 % Favored : 96.01 % Rotamer: Outliers : 4.07 % Allowed : 19.98 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -1.85 (0.09), residues: 7200 helix: 0.15 (0.11), residues: 1950 sheet: -1.41 (0.10), residues: 2445 loop : -1.91 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 350 HIS 0.005 0.002 HIS K 133 PHE 0.022 0.002 PHE C 393 TYR 0.027 0.002 TYR K 134 ARG 0.007 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 773 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.4884 (tp) REVERT: A 365 PRO cc_start: 0.5123 (Cg_endo) cc_final: 0.4842 (Cg_exo) REVERT: B 482 VAL cc_start: 0.6210 (OUTLIER) cc_final: 0.5366 (t) REVERT: C 172 LEU cc_start: 0.6465 (mt) cc_final: 0.6123 (tp) REVERT: D 172 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6808 (mm) REVERT: E 297 ASP cc_start: 0.6572 (t70) cc_final: 0.6334 (t0) REVERT: E 336 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (m) REVERT: E 445 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7817 (tm-30) REVERT: F 100 MET cc_start: 0.2184 (mmm) cc_final: 0.1655 (mmm) REVERT: F 224 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7286 (mtt180) REVERT: F 421 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7904 (tt) REVERT: G 490 VAL cc_start: 0.8401 (t) cc_final: 0.8109 (m) REVERT: G 579 ASN cc_start: 0.6004 (t0) cc_final: 0.5745 (t0) REVERT: H 579 ASN cc_start: 0.6207 (t0) cc_final: 0.5865 (t0) REVERT: I 407 MET cc_start: 0.2882 (tpp) cc_final: 0.2600 (tpt) REVERT: I 445 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: J 396 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6259 (ptm) REVERT: K 100 MET cc_start: 0.2347 (ttt) cc_final: 0.2124 (ttt) REVERT: K 335 ILE cc_start: 0.8343 (mp) cc_final: 0.8108 (mp) REVERT: L 251 TYR cc_start: 0.6439 (m-80) cc_final: 0.5943 (m-80) REVERT: L 392 ASN cc_start: 0.6248 (t0) cc_final: 0.6042 (t0) REVERT: L 529 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8153 (tp) REVERT: M 251 TYR cc_start: 0.6681 (m-80) cc_final: 0.6047 (m-80) REVERT: M 465 THR cc_start: 0.7063 (OUTLIER) cc_final: 0.6712 (p) REVERT: N 251 TYR cc_start: 0.6809 (m-80) cc_final: 0.6042 (m-80) REVERT: O 251 TYR cc_start: 0.6713 (m-80) cc_final: 0.6074 (m-80) outliers start: 246 outliers final: 147 residues processed: 952 average time/residue: 0.4897 time to fit residues: 812.3101 Evaluate side-chains 791 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 635 time to evaluate : 4.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 534 THR Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain G residue 574 ILE Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 350 TRP Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 445 GLN Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 350 TRP Chi-restraints excluded: chain J residue 396 MET Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 534 THR Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 550 LEU Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 534 THR Chi-restraints excluded: chain L residue 550 LEU Chi-restraints excluded: chain L residue 559 ASN Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 465 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 534 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 298 GLU Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 349 optimal weight: 9.9990 chunk 398 optimal weight: 0.3980 chunk 522 optimal weight: 4.9990 chunk 699 optimal weight: 9.9990 chunk 491 optimal weight: 5.9990 chunk 462 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 280 optimal weight: 2.9990 chunk 469 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN B 345 ASN D 188 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN H 133 HIS H 533 GLN I 345 ASN J 345 ASN J 533 GLN K 233 GLN ** K 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN N 188 ASN N 233 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.219568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.205764 restraints weight = 68948.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.204381 restraints weight = 119256.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.203964 restraints weight = 60259.348| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 55485 Z= 0.341 Angle : 0.760 13.065 75255 Z= 0.386 Chirality : 0.048 0.206 9120 Planarity : 0.006 0.091 9855 Dihedral : 5.967 57.866 7792 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.92 % Favored : 93.67 % Rotamer: Outliers : 4.60 % Allowed : 21.22 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.07 (0.09), residues: 7200 helix: 0.08 (0.11), residues: 1995 sheet: -1.64 (0.10), residues: 2610 loop : -2.04 (0.11), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 350 HIS 0.005 0.002 HIS A 133 PHE 0.022 0.002 PHE A 507 TYR 0.024 0.002 TYR L 134 ARG 0.010 0.001 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 278 poor density : 694 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.4927 (tp) REVERT: A 365 PRO cc_start: 0.5317 (Cg_endo) cc_final: 0.5005 (Cg_exo) REVERT: C 421 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7998 (tt) REVERT: D 167 VAL cc_start: 0.6668 (t) cc_final: 0.6437 (p) REVERT: D 473 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7779 (t) REVERT: E 421 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7705 (tt) REVERT: F 100 MET cc_start: 0.2147 (mmm) cc_final: 0.1935 (mmm) REVERT: F 224 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7351 (mtt180) REVERT: F 358 THR cc_start: 0.4482 (OUTLIER) cc_final: 0.4106 (p) REVERT: F 421 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8005 (tt) REVERT: F 481 SER cc_start: 0.6696 (m) cc_final: 0.6205 (p) REVERT: G 224 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7290 (mtt180) REVERT: G 579 ASN cc_start: 0.6168 (t0) cc_final: 0.5912 (t0) REVERT: H 100 MET cc_start: 0.1020 (ttt) cc_final: 0.0395 (mmm) REVERT: H 224 ARG cc_start: 0.7213 (mtt180) cc_final: 0.6846 (mtt-85) REVERT: H 300 THR cc_start: 0.7240 (OUTLIER) cc_final: 0.6972 (p) REVERT: H 376 ASP cc_start: 0.4495 (p0) cc_final: 0.4121 (m-30) REVERT: I 407 MET cc_start: 0.2892 (tpp) cc_final: 0.2566 (tpt) REVERT: I 445 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: J 396 MET cc_start: 0.6698 (tmm) cc_final: 0.6479 (ptm) REVERT: L 251 TYR cc_start: 0.6670 (m-80) cc_final: 0.6046 (m-80) REVERT: M 251 TYR cc_start: 0.6840 (m-80) cc_final: 0.6347 (m-80) REVERT: M 441 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7113 (mm-30) REVERT: M 529 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8333 (tt) REVERT: N 251 TYR cc_start: 0.6631 (m-80) cc_final: 0.5881 (m-80) REVERT: O 251 TYR cc_start: 0.6852 (m-80) cc_final: 0.6221 (m-80) outliers start: 278 outliers final: 192 residues processed: 901 average time/residue: 0.4840 time to fit residues: 758.0478 Evaluate side-chains 805 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 604 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 559 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 557 THR Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain H residue 573 THR Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 350 TRP Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 445 GLN Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 531 ASP Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 534 THR Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain J residue 567 MET Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 557 THR Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 534 THR Chi-restraints excluded: chain L residue 550 LEU Chi-restraints excluded: chain L residue 557 THR Chi-restraints excluded: chain L residue 559 ASN Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 350 TRP Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 445 GLN Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 512 VAL Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 534 THR Chi-restraints excluded: chain N residue 557 THR Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 298 GLU Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 551 optimal weight: 8.9990 chunk 714 optimal weight: 9.9990 chunk 379 optimal weight: 1.9990 chunk 719 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 340 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN C 308 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 308 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN E 533 GLN F 186 ASN F 233 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 533 GLN J 533 GLN K 109 ASN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 345 ASN L 533 GLN M 213 ASN ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN N 213 ASN ** N 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 602 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.213729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.198911 restraints weight = 69445.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.197493 restraints weight = 130729.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.196977 restraints weight = 66679.326| |-----------------------------------------------------------------------------| r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.6252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 55485 Z= 0.398 Angle : 0.818 13.646 75255 Z= 0.418 Chirality : 0.051 0.198 9120 Planarity : 0.006 0.089 9855 Dihedral : 6.308 59.956 7790 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.67 % Favored : 91.92 % Rotamer: Outliers : 5.34 % Allowed : 21.26 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.40 (0.09), residues: 7200 helix: 0.00 (0.11), residues: 2010 sheet: -1.86 (0.10), residues: 2475 loop : -2.40 (0.10), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 350 HIS 0.006 0.002 HIS A 133 PHE 0.026 0.003 PHE D 507 TYR 0.028 0.003 TYR G 581 ARG 0.012 0.001 ARG G 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 323 poor density : 670 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 LEU cc_start: 0.6244 (OUTLIER) cc_final: 0.5084 (tp) REVERT: A 365 PRO cc_start: 0.5159 (Cg_endo) cc_final: 0.4853 (Cg_exo) REVERT: B 141 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5434 (tp) REVERT: B 174 TYR cc_start: 0.4140 (m-80) cc_final: 0.3043 (t80) REVERT: B 179 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.6092 (mp0) REVERT: C 238 LEU cc_start: 0.4382 (tp) cc_final: 0.3806 (mt) REVERT: C 251 TYR cc_start: 0.6356 (m-80) cc_final: 0.5911 (m-80) REVERT: C 421 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8128 (tt) REVERT: C 433 GLU cc_start: 0.6550 (tp30) cc_final: 0.6136 (mm-30) REVERT: D 292 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6883 (mp) REVERT: E 257 MET cc_start: 0.6507 (tpp) cc_final: 0.6307 (ttt) REVERT: F 100 MET cc_start: 0.2143 (mmm) cc_final: 0.1827 (mmt) REVERT: F 358 THR cc_start: 0.4528 (OUTLIER) cc_final: 0.4202 (p) REVERT: F 421 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7888 (tp) REVERT: F 487 GLU cc_start: 0.7399 (tt0) cc_final: 0.6956 (mp0) REVERT: G 224 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7378 (mtt180) REVERT: G 292 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6447 (mp) REVERT: G 579 ASN cc_start: 0.6248 (t0) cc_final: 0.5946 (t0) REVERT: H 224 ARG cc_start: 0.7374 (mtt180) cc_final: 0.7029 (mtt-85) REVERT: H 376 ASP cc_start: 0.4324 (p0) cc_final: 0.3990 (m-30) REVERT: H 579 ASN cc_start: 0.6411 (t0) cc_final: 0.5962 (t0) REVERT: J 140 LEU cc_start: 0.2577 (OUTLIER) cc_final: 0.2273 (tp) REVERT: K 487 GLU cc_start: 0.7640 (tt0) cc_final: 0.7262 (mp0) REVERT: L 140 LEU cc_start: 0.2400 (OUTLIER) cc_final: 0.2056 (tp) REVERT: L 251 TYR cc_start: 0.6642 (m-80) cc_final: 0.6187 (m-80) REVERT: M 140 LEU cc_start: 0.2324 (OUTLIER) cc_final: 0.2093 (tp) REVERT: M 217 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6843 (t) REVERT: M 224 ARG cc_start: 0.6637 (mtt180) cc_final: 0.6351 (mtt180) REVERT: M 251 TYR cc_start: 0.6786 (m-80) cc_final: 0.6227 (m-80) REVERT: M 441 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7491 (mm-30) REVERT: N 172 LEU cc_start: 0.7321 (mt) cc_final: 0.7020 (mt) REVERT: N 251 TYR cc_start: 0.6466 (m-80) cc_final: 0.5929 (m-80) REVERT: O 183 LEU cc_start: 0.5976 (mt) cc_final: 0.5737 (mt) REVERT: O 251 TYR cc_start: 0.6775 (m-80) cc_final: 0.6253 (m-80) outliers start: 323 outliers final: 214 residues processed: 929 average time/residue: 0.4795 time to fit residues: 774.5063 Evaluate side-chains 799 residues out of total 6045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 573 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 550 LEU Chi-restraints excluded: chain D residue 559 ASN Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 217 VAL Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 349 GLN Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 557 THR Chi-restraints excluded: chain H residue 559 ASN Chi-restraints excluded: chain H residue 573 THR Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 350 TRP Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 297 ASP Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 465 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 534 THR Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 552 TYR Chi-restraints excluded: chain J residue 557 THR Chi-restraints excluded: chain J residue 559 ASN Chi-restraints excluded: chain J residue 567 MET Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 466 VAL Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 482 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 534 THR Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 557 THR Chi-restraints excluded: chain K residue 559 ASN Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 534 THR Chi-restraints excluded: chain L residue 550 LEU Chi-restraints excluded: chain L residue 557 THR Chi-restraints excluded: chain L residue 559 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 466 VAL Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 550 LEU Chi-restraints excluded: chain M residue 557 THR Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 185 THR Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 512 VAL Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 534 THR Chi-restraints excluded: chain N residue 557 THR Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 488 GLN Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 559 ASN Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.9968 > 50: distance: 73 - 79: 5.381 distance: 79 - 80: 19.912 distance: 80 - 81: 15.391 distance: 80 - 83: 13.993 distance: 81 - 82: 34.752 distance: 81 - 84: 15.060 distance: 84 - 85: 27.775 distance: 85 - 86: 11.399 distance: 86 - 87: 8.894 distance: 86 - 88: 12.031 distance: 88 - 89: 17.153 distance: 89 - 90: 7.454 distance: 90 - 91: 11.703 distance: 90 - 92: 3.636 distance: 92 - 93: 10.878 distance: 93 - 94: 9.108 distance: 94 - 95: 15.112 distance: 94 - 96: 13.381 distance: 96 - 97: 13.338 distance: 97 - 98: 6.877 distance: 97 - 100: 4.502 distance: 98 - 99: 6.639 distance: 98 - 104: 10.691 distance: 100 - 101: 14.733 distance: 101 - 102: 11.692 distance: 101 - 103: 3.575 distance: 104 - 105: 21.890 distance: 105 - 106: 10.070 distance: 105 - 108: 15.715 distance: 106 - 107: 21.588 distance: 106 - 111: 6.007 distance: 108 - 109: 10.398 distance: 108 - 110: 20.356 distance: 111 - 112: 4.325 distance: 112 - 113: 6.455 distance: 112 - 115: 10.760 distance: 113 - 114: 16.947 distance: 113 - 118: 13.545 distance: 115 - 116: 9.067 distance: 115 - 117: 31.084 distance: 118 - 119: 14.709 distance: 119 - 120: 13.084 distance: 119 - 122: 25.931 distance: 120 - 121: 16.126 distance: 120 - 128: 18.839 distance: 122 - 123: 22.465 distance: 123 - 124: 9.016 distance: 123 - 125: 14.850 distance: 124 - 126: 4.312 distance: 125 - 127: 6.347 distance: 126 - 127: 6.138 distance: 128 - 129: 19.460 distance: 129 - 130: 19.659 distance: 129 - 132: 21.944 distance: 130 - 131: 11.135 distance: 130 - 140: 7.219 distance: 132 - 133: 26.413 distance: 133 - 134: 11.171 distance: 133 - 135: 11.934 distance: 134 - 136: 12.320 distance: 135 - 137: 14.084 distance: 136 - 138: 8.725 distance: 138 - 139: 8.854 distance: 140 - 141: 13.443 distance: 141 - 142: 8.518 distance: 141 - 144: 11.424 distance: 142 - 143: 7.575 distance: 142 - 148: 12.047 distance: 144 - 145: 13.570 distance: 145 - 146: 24.476 distance: 145 - 147: 6.680