Starting phenix.real_space_refine on Mon Oct 26 20:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21bp_67557/10_2026/21bp_67557.cif Found real_map, /net/cci-nas-00/data/ceres_data/21bp_67557/10_2026/21bp_67557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21bp_67557/10_2026/21bp_67557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21bp_67557/10_2026/21bp_67557.map" model { file = "/net/cci-nas-00/data/ceres_data/21bp_67557/10_2026/21bp_67557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21bp_67557/10_2026/21bp_67557.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 102 5.16 5 C 13686 2.51 5 N 3705 2.21 5 O 4308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21801 Number of models: 1 Model: "" Number of chains: 15 Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1682 Classifications: {'peptide': 226} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 211} Chain: "C" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1577 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 195} Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1682 Classifications: {'peptide': 226} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 211} Chain: "B" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "G" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1577 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 195} Chain: "A" Number of atoms: 3927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3927 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 20, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1682 Classifications: {'peptide': 226} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 211} Chain: "L" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1577 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 195} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.17, per 1000 atoms: 0.24 Number of scatterers: 21801 At special positions: 0 Unit cell: (168.96, 179.52, 200.64, 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 102 16.00 O 4308 8.00 N 3705 7.00 C 13686 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 149 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 466 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 149 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 466 " distance=2.04 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 466 " distance=2.04 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 192 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 601 " - " ASN A 11 " " NAG A 602 " - " ASN A 23 " " NAG A 603 " - " ASN A 286 " " NAG B 601 " - " ASN B 11 " " NAG B 602 " - " ASN B 23 " " NAG B 603 " - " ASN B 286 " " NAG C 601 " - " ASN C 11 " " NAG C 602 " - " ASN C 23 " " NAG C 603 " - " ASN C 286 " " NAG I 1 " - " ASN C 165 " " NAG J 1 " - " ASN B 165 " " NAG K 1 " - " ASN A 165 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5136 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 72 sheets defined 17.7% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'D' and resid 88 through 92 removed outlier: 4.211A pdb=" N THR D 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.932A pdb=" N PHE C 70 " --> pdb=" O CYS C 67 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE C 71 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 369 through 388 Processing helix chain 'C' and resid 403 through 456 Processing helix chain 'C' and resid 474 through 484 Processing helix chain 'C' and resid 487 through 499 removed outlier: 4.122A pdb=" N TYR C 491 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLU C 494 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.567A pdb=" N ALA E 28 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.587A pdb=" N ALA E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 187 removed outlier: 3.587A pdb=" N HIS E 187 " --> pdb=" O GLN E 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.749A pdb=" N ASP F 91 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR F 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 92' Processing helix chain 'F' and resid 196 through 198 No H-bonds generated for 'chain 'F' and resid 196 through 198' Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.768A pdb=" N ILE B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.895A pdb=" N TRP B 122 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 Processing helix chain 'B' and resid 366 through 388 Processing helix chain 'B' and resid 403 through 455 removed outlier: 3.782A pdb=" N TYR B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 484 removed outlier: 3.776A pdb=" N MET B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 499 removed outlier: 3.578A pdb=" N ALA B 495 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 28 removed outlier: 4.220A pdb=" N ALA G 28 " --> pdb=" O ASP G 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 25 through 28' Processing helix chain 'G' and resid 78 through 82 removed outlier: 4.052A pdb=" N GLU G 82 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 125 removed outlier: 3.540A pdb=" N LEU G 124 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 120 through 125' Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.768A pdb=" N ILE A 71 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.895A pdb=" N TRP A 122 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 366 through 388 Processing helix chain 'A' and resid 403 through 455 removed outlier: 3.783A pdb=" N TYR A 423 " --> pdb=" O ASP A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.775A pdb=" N MET A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 499 removed outlier: 3.577A pdb=" N ALA A 495 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 4.211A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.567A pdb=" N ALA L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 126 removed outlier: 3.587A pdb=" N ALA L 126 " --> pdb=" O GLU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 187 removed outlier: 3.587A pdb=" N HIS L 187 " --> pdb=" O GLN L 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.572A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE D 80 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.226A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 60 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 98 through 103 removed outlier: 4.038A pdb=" N HIS D 111 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET D 101 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU D 109 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU D 103 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.913A pdb=" N GLY D 148 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 147 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS D 149 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER D 189 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL D 190 " --> pdb=" O HIS D 173 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133 removed outlier: 3.913A pdb=" N GLY D 148 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR D 185 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 186 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 178 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 160 through 163 removed outlier: 4.397A pdb=" N TYR D 203 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 362 through 365 removed outlier: 3.608A pdb=" N HIS C 355 " --> pdb=" O GLY C 362 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 352 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 6 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB1, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB2, first strand: chain 'C' and resid 41 through 44 removed outlier: 8.001A pdb=" N LEU C 41 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 276 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ASP C 43 " --> pdb=" O THR C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.802A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE C 79 " --> pdb=" O MET C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.654A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU C 175 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TYR C 252 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 257 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS C 110 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS C 259 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE C 108 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 95 removed outlier: 6.654A pdb=" N SER C 94 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N TRP C 230 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU C 175 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 132 through 137 removed outlier: 4.744A pdb=" N CYS C 135 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.535A pdb=" N VAL C 200 " --> pdb=" O GLN C 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 283 through 284 Processing sheet with id=AB9, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.477A pdb=" N VAL E 10 " --> pdb=" O THR E 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 17 through 23 Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 47 removed outlier: 6.780A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 88 through 89 removed outlier: 3.563A pdb=" N SER E 89 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.687A pdb=" N VAL E 132 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR E 171 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 113 through 117 removed outlier: 3.687A pdb=" N VAL E 132 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR E 171 " --> pdb=" O ASP E 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 152 through 154 removed outlier: 4.163A pdb=" N TRP E 147 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.706A pdb=" N PHE F 80 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.627A pdb=" N ALA F 12 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TRP F 35 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE F 51 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TRP F 37 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.627A pdb=" N ALA F 12 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS F 97 " --> pdb=" O TRP F 112 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TRP F 112 " --> pdb=" O CYS F 97 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG F 99 " --> pdb=" O ASP F 110 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 131 through 133 removed outlier: 3.789A pdb=" N GLY F 148 " --> pdb=" O LEU F 133 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 147 " --> pdb=" O VAL F 191 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS F 149 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER F 189 " --> pdb=" O CYS F 149 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR F 185 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL F 190 " --> pdb=" O HIS F 173 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 160 through 163 removed outlier: 4.431A pdb=" N TYR F 203 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.980A pdb=" N ILE B 3 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE B 467 " --> pdb=" O ILE B 3 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.570A pdb=" N GLY B 6 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 352 " --> pdb=" O GLY B 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 14 through 16 removed outlier: 4.246A pdb=" N GLU B 14 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AD7, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AD8, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.953A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 79 " --> pdb=" O MET B 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.638A pdb=" N SER B 94 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N TRP B 230 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU B 175 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR B 252 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL B 257 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS B 110 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS B 259 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 108 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.638A pdb=" N SER B 94 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N TRP B 230 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 175 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 125 through 126 Processing sheet with id=AE3, first strand: chain 'B' and resid 132 through 137 removed outlier: 4.657A pdb=" N CYS B 135 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AE5, first strand: chain 'B' and resid 278 through 280 removed outlier: 4.087A pdb=" N CYS B 278 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.541A pdb=" N THR G 103 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG G 36 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU G 45 " --> pdb=" O ARG G 36 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AE8, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AE9, first strand: chain 'G' and resid 113 through 117 removed outlier: 6.229A pdb=" N TYR G 171 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 113 through 117 removed outlier: 6.229A pdb=" N TYR G 171 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 152 through 154 removed outlier: 4.368A pdb=" N TRP G 147 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.980A pdb=" N ILE A 3 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A 467 " --> pdb=" O ILE A 3 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 6 through 7 removed outlier: 3.571A pdb=" N GLY A 6 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 352 " --> pdb=" O GLY A 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.245A pdb=" N GLU A 14 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AF7, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AF8, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.954A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 79 " --> pdb=" O MET A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.639A pdb=" N SER A 94 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N TRP A 230 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A 175 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR A 252 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 257 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N HIS A 110 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS A 259 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 108 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.639A pdb=" N SER A 94 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N TRP A 230 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 175 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 125 through 126 Processing sheet with id=AG3, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.657A pdb=" N CYS A 135 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 160 through 165 Processing sheet with id=AG5, first strand: chain 'A' and resid 278 through 280 removed outlier: 4.087A pdb=" N CYS A 278 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.573A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.227A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER H 60 " --> pdb=" O PHE H 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 98 through 103 removed outlier: 4.038A pdb=" N HIS H 111 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET H 101 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LEU H 109 " --> pdb=" O MET H 101 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU H 103 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.913A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU H 147 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS H 149 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER H 189 " --> pdb=" O CYS H 149 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL H 190 " --> pdb=" O HIS H 173 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.913A pdb=" N GLY H 148 " --> pdb=" O LEU H 133 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER H 186 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL H 178 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 160 through 163 removed outlier: 4.397A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.950A pdb=" N VAL L 10 " --> pdb=" O THR L 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AH5, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.780A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 88 through 89 removed outlier: 3.563A pdb=" N SER L 89 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 113 through 117 removed outlier: 3.686A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR L 171 " --> pdb=" O ASP L 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 113 through 117 removed outlier: 3.686A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR L 171 " --> pdb=" O ASP L 137 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 152 through 154 removed outlier: 4.163A pdb=" N TRP L 147 " --> pdb=" O VAL L 154 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2262 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: 4.76 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4137 1.33 - 1.45: 5930 1.45 - 1.58: 12110 1.58 - 1.71: 2 1.71 - 1.83: 138 Bond restraints: 22317 Sorted by residual: bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N LEU E 105 " pdb=" CA LEU E 105 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N LYS E 109 " pdb=" CA LYS E 109 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.35e+00 bond pdb=" N PRO L 108 " pdb=" CD PRO L 108 " ideal model delta sigma weight residual 1.473 1.515 -0.042 1.40e-02 5.10e+03 8.96e+00 bond pdb=" C ASN A 166 " pdb=" O ASN A 166 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.15e-02 7.56e+03 8.79e+00 ... (remaining 22312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 30014 2.66 - 5.31: 299 5.31 - 7.97: 13 7.97 - 10.62: 2 10.62 - 13.28: 2 Bond angle restraints: 30330 Sorted by residual: angle pdb=" CA PRO L 108 " pdb=" N PRO L 108 " pdb=" CD PRO L 108 " ideal model delta sigma weight residual 112.00 98.72 13.28 1.40e+00 5.10e-01 9.00e+01 angle pdb=" N ARG E 60 " pdb=" CA ARG E 60 " pdb=" C ARG E 60 " ideal model delta sigma weight residual 114.56 109.58 4.98 1.27e+00 6.20e-01 1.54e+01 angle pdb=" N ARG L 60 " pdb=" CA ARG L 60 " pdb=" C ARG L 60 " ideal model delta sigma weight residual 114.56 109.58 4.98 1.27e+00 6.20e-01 1.54e+01 angle pdb=" N ASN A 11 " pdb=" CA ASN A 11 " pdb=" C ASN A 11 " ideal model delta sigma weight residual 113.38 108.64 4.74 1.23e+00 6.61e-01 1.49e+01 angle pdb=" C ASN A 166 " pdb=" CA ASN A 166 " pdb=" CB ASN A 166 " ideal model delta sigma weight residual 110.67 116.38 -5.71 1.52e+00 4.33e-01 1.41e+01 ... (remaining 30325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.73: 12649 21.73 - 43.45: 801 43.45 - 65.18: 82 65.18 - 86.91: 50 86.91 - 108.63: 14 Dihedral angle restraints: 13596 sinusoidal: 5571 harmonic: 8025 Sorted by residual: dihedral pdb=" CB CYS B 278 " pdb=" SG CYS B 278 " pdb=" SG CYS B 302 " pdb=" CB CYS B 302 " ideal model delta sinusoidal sigma weight residual 93.00 13.92 79.08 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS A 278 " pdb=" SG CYS A 278 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 13.92 79.08 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CB CYS B 55 " pdb=" SG CYS B 55 " pdb=" SG CYS B 67 " pdb=" CB CYS B 67 " ideal model delta sinusoidal sigma weight residual 93.00 168.53 -75.53 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 13593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3183 0.100 - 0.199: 198 0.199 - 0.299: 5 0.299 - 0.399: 0 0.399 - 0.498: 1 Chirality restraints: 3387 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.20e+01 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.78e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 11 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.20e+00 ... (remaining 3384 not shown) Planarity restraints: 3915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.159 2.00e-02 2.50e+03 1.31e-01 2.13e+02 pdb=" C7 NAG A 601 " -0.043 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.210 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 603 " -0.081 2.00e-02 2.50e+03 6.69e-02 5.60e+01 pdb=" C7 NAG A 603 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG A 603 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG A 603 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG A 603 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 103 " -0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C THR L 103 " 0.065 2.00e-02 2.50e+03 pdb=" O THR L 103 " -0.025 2.00e-02 2.50e+03 pdb=" N VAL L 104 " -0.022 2.00e-02 2.50e+03 ... (remaining 3912 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 45 2.40 - 3.03: 11840 3.03 - 3.65: 31205 3.65 - 4.28: 48752 4.28 - 4.90: 84131 Nonbonded interactions: 175973 Sorted by model distance: nonbonded pdb=" O GLU C 500 " pdb=" NH2 ARG A 496 " model vdw 1.778 3.120 nonbonded pdb=" NH2 ARG B 456 " pdb=" O LEU A 462 " model vdw 1.813 3.120 nonbonded pdb=" NH2 ARG B 496 " pdb=" OE1 GLU A 500 " model vdw 1.944 3.120 nonbonded pdb=" CD PRO L 108 " pdb=" CE1 TYR L 139 " model vdw 1.978 3.740 nonbonded pdb=" NZ LYS H 138 " pdb=" OE2 GLU L 209 " model vdw 2.018 3.120 ... (remaining 175968 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 21.750 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.003 0.078 22362 Z= 0.193 Angle : 0.630 13.280 30438 Z= 0.338 Chirality : 0.047 0.498 3387 Planarity : 0.005 0.131 3903 Dihedral : 14.488 108.634 8379 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.73 % Favored : 96.16 % Rotamer: Outliers : 0.04 % Allowed : 0.54 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2760 helix: 0.15 (0.24), residues: 427 sheet: 0.38 (0.20), residues: 767 loop : -1.05 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 53 TYR 0.013 0.001 TYR A 488 PHE 0.016 0.001 PHE H 51 TRP 0.009 0.001 TRP C 60 HIS 0.007 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.19 (22317) covalent geometry : angle 0.62236 / 0.34 (30330) SS BOND : bond 0.00362 / 0.24 ( 27) SS BOND : angle 1.77184 / 1.18 ( 54) hydrogen bonds : bond 0.23440 / 15.37 ( 783) hydrogen bonds : angle 9.18817 / 6.48 ( 2262) link_BETA1-4 : bond 0.00555 / 0.28 ( 6) link_BETA1-4 : angle 1.22232 / 0.76 ( 18) link_NAG-ASN : bond 0.00564 / 0.44 ( 12) link_NAG-ASN : angle 2.07132 / 1.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 467 PHE cc_start: 0.7349 (m-80) cc_final: 0.7081 (m-80) REVERT: A 66 MET cc_start: 0.6813 (mmm) cc_final: 0.6521 (mmt) REVERT: A 189 ASN cc_start: 0.8341 (m-40) cc_final: 0.7961 (m110) REVERT: A 289 MET cc_start: 0.8104 (mmt) cc_final: 0.7864 (mtt) REVERT: A 375 ASP cc_start: 0.8114 (m-30) cc_final: 0.7904 (m-30) REVERT: A 468 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6517 (mt-10) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.1653 time to fit residues: 50.6230 Evaluate side-chains 174 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 309 ASN C 355 HIS C 401 ASN C 454 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN B 103 HIS B 401 ASN B 410 ASN G 6 GLN G 37 GLN A 8 HIS A 103 HIS A 355 HIS A 401 ASN A 454 GLN A 458 ASN H 114 GLN H 173 HIS ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.184419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.125883 restraints weight = 25915.427| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.87 r_work: 0.2954 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 22362 Z= 0.290 Angle : 0.683 8.950 30438 Z= 0.356 Chirality : 0.048 0.203 3387 Planarity : 0.005 0.055 3903 Dihedral : 7.998 74.718 3351 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.63 % Allowed : 5.17 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2760 helix: 0.91 (0.25), residues: 431 sheet: 0.06 (0.18), residues: 863 loop : -1.11 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 60 TYR 0.022 0.002 TYR G 48 PHE 0.034 0.003 PHE D 51 TRP 0.013 0.002 TRP A 149 HIS 0.013 0.002 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.29 (22317) covalent geometry : angle 0.67370 / 0.35 (30330) SS BOND : bond 0.00536 / 0.30 ( 27) SS BOND : angle 2.05916 / 1.43 ( 54) hydrogen bonds : bond 0.06422 / 4.27 ( 783) hydrogen bonds : angle 6.58472 / 4.60 ( 2262) link_BETA1-4 : bond 0.00761 / 0.32 ( 6) link_BETA1-4 : angle 1.95448 / 1.21 ( 18) link_NAG-ASN : bond 0.00415 / 0.28 ( 12) link_NAG-ASN : angle 2.01264 / 1.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: F 210 LYS cc_start: 0.6856 (mttt) cc_final: 0.6249 (tptt) REVERT: B 478 MET cc_start: 0.7541 (mmt) cc_final: 0.7286 (mmt) REVERT: G 19 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8558 (mmtp) REVERT: A 189 ASN cc_start: 0.8868 (m-40) cc_final: 0.8451 (m110) REVERT: A 289 MET cc_start: 0.8528 (mmt) cc_final: 0.7939 (mtt) REVERT: A 478 MET cc_start: 0.7257 (mmt) cc_final: 0.6940 (mmt) REVERT: L 78 GLN cc_start: 0.7960 (mt0) cc_final: 0.7530 (mt0) REVERT: L 82 GLU cc_start: 0.7472 (pp20) cc_final: 0.7040 (pp20) outliers start: 15 outliers final: 12 residues processed: 177 average time/residue: 0.1643 time to fit residues: 44.2047 Evaluate side-chains 168 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 454 GLN Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [36, 80, 120, 247, 126, 69, 177, 15, 169, 230, 119] chunk 36 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 247 optimal weight: 30.0000 chunk 126 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 177 optimal weight: 30.0000 chunk 15 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 309 ASN C 355 HIS C 454 GLN E 30 ASN E 78 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B 410 ASN B 458 ASN A 8 HIS A 355 HIS A 410 ASN H 114 GLN L 30 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.187254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.128152 restraints weight = 25866.310| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.06 r_work: 0.3003 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22362 Z= 0.128 Angle : 0.552 6.828 30438 Z= 0.288 Chirality : 0.044 0.184 3387 Planarity : 0.004 0.046 3903 Dihedral : 6.309 56.331 3351 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.63 % Allowed : 6.76 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2760 helix: 1.41 (0.25), residues: 434 sheet: 0.11 (0.18), residues: 849 loop : -0.93 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 58 TYR 0.013 0.001 TYR A 271 PHE 0.016 0.001 PHE D 51 TRP 0.010 0.001 TRP F 48 HIS 0.012 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (22317) covalent geometry : angle 0.54350 / 0.29 (30330) SS BOND : bond 0.00392 / 0.23 ( 27) SS BOND : angle 1.68795 / 1.17 ( 54) hydrogen bonds : bond 0.04888 / 3.24 ( 783) hydrogen bonds : angle 5.84037 / 4.05 ( 2262) link_BETA1-4 : bond 0.00590 / 0.30 ( 6) link_BETA1-4 : angle 1.96807 / 1.21 ( 18) link_NAG-ASN : bond 0.00151 / 0.11 ( 12) link_NAG-ASN : angle 1.60229 / 0.96 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: C 401 ASN cc_start: 0.8202 (t0) cc_final: 0.7885 (t0) REVERT: C 483 ASN cc_start: 0.6485 (m-40) cc_final: 0.6218 (m-40) REVERT: E 82 GLU cc_start: 0.7524 (pp20) cc_final: 0.7124 (pp20) REVERT: A 189 ASN cc_start: 0.8716 (m-40) cc_final: 0.8306 (m110) REVERT: A 289 MET cc_start: 0.8421 (mmt) cc_final: 0.7811 (mtt) REVERT: A 478 MET cc_start: 0.7088 (mmt) cc_final: 0.6735 (mmt) REVERT: L 14 LEU cc_start: 0.7336 (tt) cc_final: 0.7051 (tt) REVERT: L 78 GLN cc_start: 0.7900 (mt0) cc_final: 0.7442 (mt0) REVERT: L 82 GLU cc_start: 0.7549 (pp20) cc_final: 0.6983 (pp20) outliers start: 15 outliers final: 9 residues processed: 183 average time/residue: 0.1597 time to fit residues: 44.7420 Evaluate side-chains 170 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain A residue 317 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [19, 29, 172, 131, 48, 63, 84, 202, 213, 118, 40] chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 202 optimal weight: 1.9990 chunk 213 optimal weight: 0.0870 chunk 118 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 309 ASN C 454 GLN E 78 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B 410 ASN A 8 HIS A 355 HIS A 401 ASN A 410 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.186018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127525 restraints weight = 25930.545| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.84 r_work: 0.2984 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22362 Z= 0.170 Angle : 0.565 6.982 30438 Z= 0.294 Chirality : 0.044 0.176 3387 Planarity : 0.004 0.066 3903 Dihedral : 5.410 56.973 3351 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.96 % Allowed : 8.55 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2760 helix: 1.61 (0.25), residues: 434 sheet: 0.17 (0.18), residues: 876 loop : -0.90 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 58 TYR 0.014 0.001 TYR G 48 PHE 0.023 0.002 PHE D 51 TRP 0.011 0.001 TRP F 48 HIS 0.012 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (22317) covalent geometry : angle 0.55570 / 0.29 (30330) SS BOND : bond 0.00488 / 0.28 ( 27) SS BOND : angle 1.88642 / 1.26 ( 54) hydrogen bonds : bond 0.04639 / 3.08 ( 783) hydrogen bonds : angle 5.50676 / 3.79 ( 2262) link_BETA1-4 : bond 0.00456 / 0.23 ( 6) link_BETA1-4 : angle 1.92724 / 1.18 ( 18) link_NAG-ASN : bond 0.00216 / 0.15 ( 12) link_NAG-ASN : angle 1.71462 / 1.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: C 401 ASN cc_start: 0.8204 (t0) cc_final: 0.7928 (t0) REVERT: C 404 ARG cc_start: 0.8566 (mmp-170) cc_final: 0.8243 (mmp-170) REVERT: E 82 GLU cc_start: 0.7615 (pp20) cc_final: 0.7182 (pp20) REVERT: A 189 ASN cc_start: 0.8738 (m-40) cc_final: 0.8331 (m110) REVERT: A 289 MET cc_start: 0.8490 (mmt) cc_final: 0.7891 (mtt) REVERT: A 478 MET cc_start: 0.7150 (mmt) cc_final: 0.6798 (mmt) REVERT: L 14 LEU cc_start: 0.7427 (tt) cc_final: 0.7115 (tt) REVERT: L 78 GLN cc_start: 0.7970 (mt0) cc_final: 0.7519 (mt0) REVERT: L 82 GLU cc_start: 0.7655 (pp20) cc_final: 0.7041 (pp20) outliers start: 23 outliers final: 15 residues processed: 174 average time/residue: 0.1502 time to fit residues: 40.5004 Evaluate side-chains 167 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [225, 76, 133, 87, 140, 103, 84, 209, 231, 12, 143] chunk 225 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 87 optimal weight: 40.0000 chunk 140 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 231 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 309 ASN C 454 GLN E 78 GLN F 36 ASN B 401 ASN A 8 HIS A 154 ASN A 355 HIS A 410 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.184486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125908 restraints weight = 25749.595| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.99 r_work: 0.2957 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 22362 Z= 0.226 Angle : 0.611 7.975 30438 Z= 0.316 Chirality : 0.046 0.170 3387 Planarity : 0.005 0.073 3903 Dihedral : 5.295 58.540 3351 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.38 % Allowed : 9.05 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2760 helix: 1.56 (0.25), residues: 434 sheet: 0.09 (0.18), residues: 876 loop : -1.02 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 216 TYR 0.019 0.002 TYR G 48 PHE 0.027 0.002 PHE D 51 TRP 0.014 0.002 TRP F 48 HIS 0.011 0.002 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (22317) covalent geometry : angle 0.60123 / 0.31 (30330) SS BOND : bond 0.00537 / 0.28 ( 27) SS BOND : angle 2.00377 / 1.34 ( 54) hydrogen bonds : bond 0.04832 / 3.22 ( 783) hydrogen bonds : angle 5.43416 / 3.73 ( 2262) link_BETA1-4 : bond 0.00411 / 0.20 ( 6) link_BETA1-4 : angle 1.62591 / 1.00 ( 18) link_NAG-ASN : bond 0.00352 / 0.22 ( 12) link_NAG-ASN : angle 1.92597 / 1.15 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: C 90 CYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7563 (p) REVERT: C 401 ASN cc_start: 0.8444 (t0) cc_final: 0.8129 (t0) REVERT: C 404 ARG cc_start: 0.8544 (mmp-170) cc_final: 0.8184 (mmp-170) REVERT: E 82 GLU cc_start: 0.7653 (pp20) cc_final: 0.7173 (pp20) REVERT: E 88 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.6545 (t80) REVERT: G 88 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7156 (t80) REVERT: A 13 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 189 ASN cc_start: 0.8780 (m-40) cc_final: 0.8382 (m110) REVERT: A 289 MET cc_start: 0.8470 (mmt) cc_final: 0.7819 (mtt) REVERT: A 478 MET cc_start: 0.7163 (mmt) cc_final: 0.6755 (mmt) REVERT: L 14 LEU cc_start: 0.7381 (tt) cc_final: 0.7050 (tt) REVERT: L 78 GLN cc_start: 0.8039 (mt0) cc_final: 0.7616 (mt0) REVERT: L 82 GLU cc_start: 0.7741 (pp20) cc_final: 0.7258 (pp20) REVERT: L 88 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7913 (t80) outliers start: 33 outliers final: 21 residues processed: 180 average time/residue: 0.1546 time to fit residues: 43.2137 Evaluate side-chains 178 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 90 CYS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 88 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [134, 92, 190, 56, 238, 66, 138, 113, 135, 150, 44] chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 309 ASN C 454 GLN E 78 GLN B 401 ASN A 8 HIS A 355 HIS A 401 ASN A 454 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.186200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.127390 restraints weight = 25808.879| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.97 r_work: 0.2989 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22362 Z= 0.136 Angle : 0.540 6.675 30438 Z= 0.282 Chirality : 0.043 0.171 3387 Planarity : 0.004 0.062 3903 Dihedral : 5.028 57.251 3351 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.08 % Allowed : 9.89 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2760 helix: 1.66 (0.25), residues: 440 sheet: 0.22 (0.19), residues: 822 loop : -0.97 (0.16), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 58 TYR 0.015 0.001 TYR G 31 PHE 0.019 0.002 PHE D 51 TRP 0.011 0.001 TRP F 48 HIS 0.013 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (22317) covalent geometry : angle 0.53116 / 0.28 (30330) SS BOND : bond 0.00433 / 0.24 ( 27) SS BOND : angle 1.75585 / 1.18 ( 54) hydrogen bonds : bond 0.04344 / 2.89 ( 783) hydrogen bonds : angle 5.23936 / 3.59 ( 2262) link_BETA1-4 : bond 0.00424 / 0.21 ( 6) link_BETA1-4 : angle 1.40138 / 0.85 ( 18) link_NAG-ASN : bond 0.00196 / 0.13 ( 12) link_NAG-ASN : angle 1.67690 / 0.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: C 189 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8199 (m110) REVERT: C 401 ASN cc_start: 0.8403 (t0) cc_final: 0.8106 (t0) REVERT: C 404 ARG cc_start: 0.8519 (mmp-170) cc_final: 0.8180 (mmp-170) REVERT: E 82 GLU cc_start: 0.7645 (pp20) cc_final: 0.7428 (pp20) REVERT: E 88 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.6335 (t80) REVERT: B 404 ARG cc_start: 0.8454 (mmp-170) cc_final: 0.8167 (mmp-170) REVERT: G 88 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 13 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 189 ASN cc_start: 0.8746 (m-40) cc_final: 0.8337 (m110) REVERT: A 289 MET cc_start: 0.8420 (mmt) cc_final: 0.7815 (mtt) REVERT: A 478 MET cc_start: 0.7102 (mmt) cc_final: 0.6674 (mmt) REVERT: L 14 LEU cc_start: 0.7241 (tt) cc_final: 0.6889 (tt) REVERT: L 78 GLN cc_start: 0.8041 (mt0) cc_final: 0.7574 (mt0) REVERT: L 82 GLU cc_start: 0.7812 (pp20) cc_final: 0.7406 (pp20) REVERT: L 88 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7902 (t80) outliers start: 26 outliers final: 16 residues processed: 183 average time/residue: 0.1580 time to fit residues: 44.6366 Evaluate side-chains 175 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 189 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 88 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [254, 242, 55, 203, 150, 71, 17, 207, 62, 201, 123] chunk 254 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 17 optimal weight: 50.0000 chunk 207 optimal weight: 0.0470 chunk 62 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 454 GLN E 78 GLN B 401 ASN A 355 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126889 restraints weight = 25869.826| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.00 r_work: 0.2982 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22362 Z= 0.162 Angle : 0.550 6.882 30438 Z= 0.287 Chirality : 0.044 0.170 3387 Planarity : 0.004 0.059 3903 Dihedral : 5.001 57.268 3351 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.42 % Allowed : 10.14 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.16), residues: 2760 helix: 1.70 (0.25), residues: 440 sheet: 0.20 (0.18), residues: 858 loop : -0.99 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 58 TYR 0.015 0.001 TYR D 61 PHE 0.022 0.002 PHE D 51 TRP 0.011 0.001 TRP F 48 HIS 0.011 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (22317) covalent geometry : angle 0.54182 / 0.28 (30330) SS BOND : bond 0.00450 / 0.24 ( 27) SS BOND : angle 1.73789 / 1.18 ( 54) hydrogen bonds : bond 0.04376 / 2.91 ( 783) hydrogen bonds : angle 5.17499 / 3.55 ( 2262) link_BETA1-4 : bond 0.00443 / 0.22 ( 6) link_BETA1-4 : angle 1.37727 / 0.84 ( 18) link_NAG-ASN : bond 0.00222 / 0.14 ( 12) link_NAG-ASN : angle 1.71654 / 1.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: C 401 ASN cc_start: 0.8421 (t0) cc_final: 0.8178 (t0) REVERT: E 82 GLU cc_start: 0.7654 (pp20) cc_final: 0.7389 (pp20) REVERT: E 88 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.6364 (t80) REVERT: B 404 ARG cc_start: 0.8455 (mmp-170) cc_final: 0.8170 (mmp-170) REVERT: G 88 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7098 (t80) REVERT: G 93 ASN cc_start: 0.8111 (m-40) cc_final: 0.7603 (t0) REVERT: A 13 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 189 ASN cc_start: 0.8761 (m-40) cc_final: 0.8361 (m110) REVERT: A 289 MET cc_start: 0.8469 (mmt) cc_final: 0.7814 (mtt) REVERT: A 404 ARG cc_start: 0.8492 (mmp-170) cc_final: 0.8119 (mmp-170) REVERT: A 406 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8621 (mm) REVERT: A 478 MET cc_start: 0.7095 (mmt) cc_final: 0.6668 (mmt) REVERT: L 14 LEU cc_start: 0.7243 (tt) cc_final: 0.6886 (tt) REVERT: L 78 GLN cc_start: 0.8047 (mt0) cc_final: 0.7585 (mt0) REVERT: L 82 GLU cc_start: 0.7818 (pp20) cc_final: 0.7452 (pp20) REVERT: L 88 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7924 (t80) outliers start: 34 outliers final: 21 residues processed: 182 average time/residue: 0.1563 time to fit residues: 43.2820 Evaluate side-chains 182 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 59 GLU Chi-restraints excluded: chain L residue 88 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [29, 213, 90, 169, 56, 119, 250, 12, 20, 241, 134] chunk 29 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 90 optimal weight: 0.0770 chunk 169 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 250 optimal weight: 50.0000 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 ASN C 454 GLN C 458 ASN E 78 GLN B 401 ASN A 84 ASN A 355 HIS A 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.185903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126366 restraints weight = 25767.104| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.36 r_work: 0.2984 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22362 Z= 0.156 Angle : 0.545 6.825 30438 Z= 0.284 Chirality : 0.044 0.170 3387 Planarity : 0.004 0.057 3903 Dihedral : 4.928 57.132 3351 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.25 % Allowed : 10.76 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2760 helix: 1.73 (0.25), residues: 440 sheet: 0.21 (0.18), residues: 858 loop : -0.97 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 456 TYR 0.015 0.001 TYR G 48 PHE 0.021 0.002 PHE D 51 TRP 0.012 0.001 TRP F 48 HIS 0.011 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (22317) covalent geometry : angle 0.53692 / 0.28 (30330) SS BOND : bond 0.00440 / 0.24 ( 27) SS BOND : angle 1.72906 / 1.17 ( 54) hydrogen bonds : bond 0.04290 / 2.86 ( 783) hydrogen bonds : angle 5.07467 / 3.47 ( 2262) link_BETA1-4 : bond 0.00447 / 0.22 ( 6) link_BETA1-4 : angle 1.30764 / 0.80 ( 18) link_NAG-ASN : bond 0.00224 / 0.14 ( 12) link_NAG-ASN : angle 1.71951 / 1.02 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: C 401 ASN cc_start: 0.8435 (t0) cc_final: 0.8114 (t0) REVERT: C 404 ARG cc_start: 0.8473 (mmp-170) cc_final: 0.8077 (mmp-170) REVERT: E 82 GLU cc_start: 0.7758 (pp20) cc_final: 0.7155 (pp20) REVERT: E 88 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.6292 (t80) REVERT: G 88 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7092 (t80) REVERT: G 93 ASN cc_start: 0.8149 (m-40) cc_final: 0.7670 (t0) REVERT: A 13 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.8967 (p) REVERT: A 189 ASN cc_start: 0.8758 (m-40) cc_final: 0.8361 (m110) REVERT: A 289 MET cc_start: 0.8464 (mmt) cc_final: 0.7814 (mtt) REVERT: A 404 ARG cc_start: 0.8455 (mmp-170) cc_final: 0.8091 (mmp-170) REVERT: A 406 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8584 (mm) REVERT: L 14 LEU cc_start: 0.7229 (tt) cc_final: 0.6873 (tt) REVERT: L 78 GLN cc_start: 0.8040 (mt0) cc_final: 0.7595 (mt0) REVERT: L 82 GLU cc_start: 0.7858 (pp20) cc_final: 0.7534 (pp20) REVERT: L 88 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7811 (t80) outliers start: 30 outliers final: 20 residues processed: 184 average time/residue: 0.1554 time to fit residues: 43.9377 Evaluate side-chains 177 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 88 TYR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain L residue 88 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [35, 275, 273, 23, 62, 186, 257, 55, 198, 133, 37] chunk 35 optimal weight: 1.9990 chunk 275 optimal weight: 0.1980 chunk 273 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 257 optimal weight: 0.0270 chunk 55 optimal weight: 4.9990 chunk 198 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN E 78 GLN B 401 ASN A 355 HIS A 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.188416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.129714 restraints weight = 25827.980| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.96 r_work: 0.3042 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 22362 Z= 0.098 Angle : 0.498 5.774 30438 Z= 0.260 Chirality : 0.042 0.175 3387 Planarity : 0.004 0.057 3903 Dihedral : 4.633 55.407 3351 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.96 % Allowed : 11.39 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2760 helix: 1.94 (0.25), residues: 440 sheet: 0.34 (0.19), residues: 819 loop : -0.84 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 456 TYR 0.013 0.001 TYR H 61 PHE 0.023 0.001 PHE L 138 TRP 0.011 0.001 TRP C 421 HIS 0.011 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (22317) covalent geometry : angle 0.49172 / 0.26 (30330) SS BOND : bond 0.00421 / 0.26 ( 27) SS BOND : angle 1.50524 / 1.02 ( 54) hydrogen bonds : bond 0.03795 / 2.52 ( 783) hydrogen bonds : angle 4.88370 / 3.35 ( 2262) link_BETA1-4 : bond 0.00490 / 0.25 ( 6) link_BETA1-4 : angle 1.24001 / 0.76 ( 18) link_NAG-ASN : bond 0.00135 / 0.08 ( 12) link_NAG-ASN : angle 1.41329 / 0.84 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: C 308 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8494 (m) REVERT: C 401 ASN cc_start: 0.8404 (t0) cc_final: 0.8030 (t0) REVERT: E 82 GLU cc_start: 0.7751 (pp20) cc_final: 0.7114 (pp20) REVERT: B 7 TYR cc_start: 0.9001 (p90) cc_final: 0.8780 (p90) REVERT: B 483 ASN cc_start: 0.6291 (m-40) cc_final: 0.5982 (m-40) REVERT: G 88 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.6889 (t80) REVERT: G 93 ASN cc_start: 0.8124 (m-40) cc_final: 0.7717 (t0) REVERT: A 13 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8627 (p) REVERT: A 66 MET cc_start: 0.7165 (mmm) cc_final: 0.6897 (mpp) REVERT: A 189 ASN cc_start: 0.8694 (m-40) cc_final: 0.8286 (m110) REVERT: A 289 MET cc_start: 0.8402 (mmt) cc_final: 0.7700 (mtt) REVERT: A 404 ARG cc_start: 0.8380 (mmp-170) cc_final: 0.8147 (mmp-170) REVERT: A 406 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8606 (mm) REVERT: L 78 GLN cc_start: 0.8050 (mt0) cc_final: 0.7561 (mt0) REVERT: L 82 GLU cc_start: 0.7860 (pp20) cc_final: 0.7572 (pp20) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.1543 time to fit residues: 44.6840 Evaluate side-chains 179 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 88 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [102, 127, 187, 251, 50, 226, 24, 168, 100, 164, 90] chunk 102 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 187 optimal weight: 0.0170 chunk 251 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 168 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 164 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN E 78 GLN F 79 HIS B 401 ASN A 355 HIS A 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130659 restraints weight = 25898.910| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.92 r_work: 0.3047 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 22362 Z= 0.095 Angle : 0.493 5.547 30438 Z= 0.257 Chirality : 0.042 0.191 3387 Planarity : 0.004 0.057 3903 Dihedral : 4.524 54.954 3351 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.71 % Allowed : 11.97 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2760 helix: 2.11 (0.25), residues: 440 sheet: 0.43 (0.19), residues: 819 loop : -0.74 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 456 TYR 0.011 0.001 TYR F 33 PHE 0.021 0.001 PHE E 138 TRP 0.010 0.001 TRP C 421 HIS 0.011 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (22317) covalent geometry : angle 0.48643 / 0.25 (30330) SS BOND : bond 0.00348 / 0.20 ( 27) SS BOND : angle 1.43013 / 0.96 ( 54) hydrogen bonds : bond 0.03681 / 2.45 ( 783) hydrogen bonds : angle 4.78390 / 3.27 ( 2262) link_BETA1-4 : bond 0.00456 / 0.23 ( 6) link_BETA1-4 : angle 1.27917 / 0.77 ( 18) link_NAG-ASN : bond 0.00133 / 0.08 ( 12) link_NAG-ASN : angle 1.38989 / 0.83 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: C 308 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8499 (m) REVERT: C 401 ASN cc_start: 0.8402 (t0) cc_final: 0.8035 (t0) REVERT: E 82 GLU cc_start: 0.7752 (pp20) cc_final: 0.7115 (pp20) REVERT: B 7 TYR cc_start: 0.8994 (p90) cc_final: 0.8772 (p90) REVERT: B 404 ARG cc_start: 0.8395 (mmp-170) cc_final: 0.8038 (mmp-170) REVERT: B 483 ASN cc_start: 0.6197 (m-40) cc_final: 0.5856 (m-40) REVERT: G 93 ASN cc_start: 0.8121 (m-40) cc_final: 0.7725 (t0) REVERT: A 13 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8606 (p) REVERT: A 66 MET cc_start: 0.7206 (mmm) cc_final: 0.6776 (mpp) REVERT: A 189 ASN cc_start: 0.8681 (m-40) cc_final: 0.8287 (m110) REVERT: A 406 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8614 (mm) REVERT: L 78 GLN cc_start: 0.8060 (mt0) cc_final: 0.7587 (mt0) REVERT: L 82 GLU cc_start: 0.7907 (pp20) cc_final: 0.7577 (pp20) outliers start: 17 outliers final: 12 residues processed: 184 average time/residue: 0.1579 time to fit residues: 44.3523 Evaluate side-chains 180 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 308 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 135 CYS Chi-restraints excluded: chain A residue 406 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: [266, 97, 69, 120, 75, 54, 87, 270, 228, 218, 180] chunk 266 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 54 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.7608 > 50:) chunk 87 optimal weight: 0.8980 chunk 270 optimal weight: 6.9990 chunk 228 optimal weight: 0.9980 chunk 218 optimal weight: 7.9990 chunk 180 optimal weight: 30.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN B 401 ASN A 84 ASN A 355 HIS A 454 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.128317 restraints weight = 25653.207| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.76 r_work: 0.2974 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22362 Z= 0.177 Angle : 0.559 6.872 30438 Z= 0.290 Chirality : 0.044 0.187 3387 Planarity : 0.004 0.057 3903 Dihedral : 4.836 57.332 3351 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.79 % Allowed : 11.97 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2760 helix: 1.99 (0.25), residues: 440 sheet: 0.30 (0.18), residues: 870 loop : -0.80 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 456 TYR 0.024 0.001 TYR F 33 PHE 0.025 0.002 PHE D 51 TRP 0.011 0.001 TRP F 48 HIS 0.010 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (22317) covalent geometry : angle 0.55056 / 0.29 (30330) SS BOND : bond 0.00523 / 0.32 ( 27) SS BOND : angle 1.76724 / 1.16 ( 54) hydrogen bonds : bond 0.04255 / 2.85 ( 783) hydrogen bonds : angle 4.92525 / 3.37 ( 2262) link_BETA1-4 : bond 0.00413 / 0.20 ( 6) link_BETA1-4 : angle 1.32980 / 0.81 ( 18) link_NAG-ASN : bond 0.00258 / 0.16 ( 12) link_NAG-ASN : angle 1.74386 / 1.04 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8333.03 seconds wall clock time: 142 minutes 25.67 seconds (8545.67 seconds total)