Starting phenix.real_space_refine on Sun Apr 14 14:10:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7s_36047/04_2024/8j7s_36047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7s_36047/04_2024/8j7s_36047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7s_36047/04_2024/8j7s_36047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7s_36047/04_2024/8j7s_36047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7s_36047/04_2024/8j7s_36047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7s_36047/04_2024/8j7s_36047.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 163 5.49 5 S 92 5.16 5 C 20019 2.51 5 N 5322 2.21 5 O 6216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 79": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 289": "OE1" <-> "OE2" Residue "J TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 406": "OE1" <-> "OE2" Residue "M GLU 488": "OE1" <-> "OE2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "N TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 399": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3634 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3479 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "D" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 413 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3636 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3475 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "H" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "I" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3633 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "J" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3461 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "K" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 454 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "M" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3629 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3472 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "P" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N PHE A 238 " occ=0.23 ... (9 atoms not shown) pdb=" CZ PHE A 238 " occ=0.02 residue: pdb=" N GLY A 239 " occ=0.32 ... (2 atoms not shown) pdb=" O GLY A 239 " occ=0.20 residue: pdb=" N MET B 193 " occ=0.66 ... (6 atoms not shown) pdb=" CE MET B 193 " occ=0.35 residue: pdb=" N PRO B 195 " occ=0.13 ... (5 atoms not shown) pdb=" CD PRO B 195 " occ=0.77 residue: pdb=" N ASP B 199 " occ=0.47 ... (6 atoms not shown) pdb=" OD2 ASP B 199 " occ=0.87 residue: pdb=" N GLU B 296 " occ=0.63 ... (7 atoms not shown) pdb=" OE2 GLU B 296 " occ=0.57 residue: pdb=" N ASP B 346 " occ=0.92 ... (6 atoms not shown) pdb=" OD2 ASP B 346 " occ=0.55 residue: pdb=" N GLY B 396 " occ=0.26 ... (2 atoms not shown) pdb=" O GLY B 396 " occ=0.38 residue: pdb=" N GLY E 102 " occ=0.54 ... (2 atoms not shown) pdb=" O GLY E 102 " occ=0.07 residue: pdb=" N ALA E 237 " occ=0.11 ... (3 atoms not shown) pdb=" CB ALA E 237 " occ=0.21 residue: pdb=" N GLY E 239 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY E 239 " occ=0.74 residue: pdb=" N SER F 250 " occ=0.67 ... (4 atoms not shown) pdb=" OG SER F 250 " occ=0.09 ... (remaining 4 not shown) Time building chain proxies: 17.63, per 1000 atoms: 0.55 Number of scatterers: 31812 At special positions: 0 Unit cell: (134.662, 171.291, 225.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 163 15.00 O 6216 8.00 N 5322 7.00 C 20019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.04 Conformation dependent library (CDL) restraints added in 5.8 seconds 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6640 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 36 sheets defined 35.4% alpha, 14.5% beta 58 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 11.16 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.652A pdb=" N ILE A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 110 through 131 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.520A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 14 through 29 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 123 through 139 removed outlier: 3.687A pdb=" N GLY B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.057A pdb=" N PHE B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 removed outlier: 4.109A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 257 through 277 removed outlier: 3.664A pdb=" N MET B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 369 through 384 removed outlier: 3.596A pdb=" N LEU B 384 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.559A pdb=" N GLY E 90 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 97 through 106 removed outlier: 3.661A pdb=" N ILE E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 131 Processing helix chain 'E' and resid 206 through 214 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 264 Processing helix chain 'E' and resid 331 through 351 removed outlier: 4.239A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 376 removed outlier: 3.614A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 Processing helix chain 'E' and resid 477 through 491 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'F' and resid 14 through 28 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 71 through 89 Processing helix chain 'F' and resid 109 through 113 Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 146 through 158 removed outlier: 4.268A pdb=" N SER F 150 " --> pdb=" O ASP F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 4.007A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 257 through 279 removed outlier: 3.753A pdb=" N LYS F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 365 Processing helix chain 'F' and resid 369 through 385 removed outlier: 3.662A pdb=" N LEU F 384 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 385 " --> pdb=" O ILE F 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 31 removed outlier: 3.615A pdb=" N GLY I 26 " --> pdb=" O ASP I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 62 removed outlier: 3.897A pdb=" N LYS I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 83 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.555A pdb=" N PHE I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR I 106 " --> pdb=" O GLY I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 131 Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 248 through 264 Processing helix chain 'I' and resid 331 through 351 removed outlier: 3.685A pdb=" N GLN I 349 " --> pdb=" O SER I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.729A pdb=" N VAL I 376 " --> pdb=" O ALA I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 462 Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.578A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'J' and resid 14 through 29 Processing helix chain 'J' and resid 44 through 56 Processing helix chain 'J' and resid 71 through 89 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 123 through 139 Processing helix chain 'J' and resid 149 through 157 removed outlier: 4.024A pdb=" N LEU J 153 " --> pdb=" O LYS J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.769A pdb=" N GLU J 202 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.786A pdb=" N THR J 230 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU J 231 " --> pdb=" O PRO J 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 227 through 231' Processing helix chain 'J' and resid 257 through 277 Processing helix chain 'J' and resid 353 through 365 Processing helix chain 'J' and resid 369 through 384 removed outlier: 3.512A pdb=" N TRP J 373 " --> pdb=" O TRP J 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 22 through 30 Processing helix chain 'M' and resid 46 through 60 Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 87 through 89 No H-bonds generated for 'chain 'M' and resid 87 through 89' Processing helix chain 'M' and resid 97 through 106 removed outlier: 3.819A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 131 removed outlier: 3.784A pdb=" N THR M 114 " --> pdb=" O THR M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 213 Processing helix chain 'M' and resid 226 through 230 Processing helix chain 'M' and resid 248 through 264 Processing helix chain 'M' and resid 331 through 351 removed outlier: 3.708A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 376 Processing helix chain 'M' and resid 427 through 430 Processing helix chain 'M' and resid 451 through 463 Processing helix chain 'M' and resid 477 through 491 removed outlier: 3.533A pdb=" N THR M 491 " --> pdb=" O GLY M 487 " (cutoff:3.500A) Processing helix chain 'M' and resid 502 through 506 Processing helix chain 'N' and resid 14 through 28 Processing helix chain 'N' and resid 45 through 56 Processing helix chain 'N' and resid 71 through 89 Processing helix chain 'N' and resid 123 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.144A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 233 removed outlier: 3.585A pdb=" N GLU N 231 " --> pdb=" O PRO N 228 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR N 233 " --> pdb=" O THR N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 278 removed outlier: 3.603A pdb=" N CYS N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS N 262 " --> pdb=" O ASN N 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG N 263 " --> pdb=" O ALA N 259 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS N 278 " --> pdb=" O GLU N 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 353 through 366 removed outlier: 3.600A pdb=" N LYS N 366 " --> pdb=" O ARG N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 369 through 384 removed outlier: 3.798A pdb=" N TRP N 373 " --> pdb=" O TRP N 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.337A pdb=" N LYS A 2 " --> pdb=" O LYS B 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 6 removed outlier: 4.925A pdb=" N VAL A 412 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE A 419 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 417 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 443 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER A 389 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.439A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.753A pdb=" N THR A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.571A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 175 through 179 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 175 through 179 current: chain 'B' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 291 through 294 current: chain 'B' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 334 through 344 current: chain 'B' and resid 400 through 404 Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 209 Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 3 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 2 through 3 current: chain 'F' and resid 169 through 179 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 179 current: chain 'F' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 291 through 294 current: chain 'F' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 334 through 344 current: chain 'F' and resid 400 through 412 Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 5 through 6 current: chain 'E' and resid 297 through 305 removed outlier: 3.751A pdb=" N LEU E 305 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 312 " --> pdb=" O LEU E 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 312 through 313 current: chain 'E' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 382 through 389 current: chain 'E' and resid 417 through 420 Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.534A pdb=" N GLN E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 94 through 95 removed outlier: 7.863A pdb=" N LYS E 94 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL E 43 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL E 141 " --> pdb=" O PHE E 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 425 through 426 Processing sheet with id=AB6, first strand: chain 'F' and resid 32 through 33 removed outlier: 7.115A pdb=" N LYS F 4 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE F 60 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE F 6 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU F 62 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER F 8 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER F 64 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ILE F 118 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 208 through 209 Processing sheet with id=AB8, first strand: chain 'I' and resid 2 through 3 removed outlier: 5.800A pdb=" N LYS I 2 " --> pdb=" O LYS J 411 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 5 through 6 current: chain 'I' and resid 297 through 305 removed outlier: 3.631A pdb=" N VAL I 312 " --> pdb=" O LEU I 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 312 through 313 current: chain 'I' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 382 through 389 current: chain 'I' and resid 417 through 420 Processing sheet with id=AC1, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.544A pdb=" N LYS I 270 " --> pdb=" O LEU I 13 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 95 removed outlier: 6.044A pdb=" N GLY I 42 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE I 142 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE I 44 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP I 139 " --> pdb=" O GLN I 222 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE I 224 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL I 141 " --> pdb=" O PHE I 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 425 through 426 removed outlier: 3.579A pdb=" N THR I 431 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 31 through 33 removed outlier: 6.997A pdb=" N LYS J 4 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU J 61 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE J 6 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL J 63 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER J 8 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ILE J 95 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE J 60 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AC6, first strand: chain 'J' and resid 208 through 209 removed outlier: 4.096A pdb=" N VAL J 208 " --> pdb=" O CYS J 215 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS J 215 " --> pdb=" O VAL J 208 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 283 through 286 Processing sheet with id=AC8, first strand: chain 'J' and resid 390 through 394 Processing sheet with id=AC9, first strand: chain 'M' and resid 2 through 3 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 3 current: chain 'N' and resid 169 through 179 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 169 through 179 current: chain 'N' and resid 318 through 328 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 334 through 344 current: chain 'N' and resid 400 through 412 Processing sheet with id=AD1, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.619A pdb=" N GLN M 18 " --> pdb=" O PHE M 14 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 91 through 95 removed outlier: 7.132A pdb=" N SER M 41 " --> pdb=" O THR M 92 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LYS M 94 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL M 43 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP M 139 " --> pdb=" O GLN M 222 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N PHE M 224 " --> pdb=" O TRP M 139 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL M 141 " --> pdb=" O PHE M 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 278 through 287 removed outlier: 3.614A pdb=" N VAL M 312 " --> pdb=" O LEU M 305 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 312 through 313 current: chain 'M' and resid 382 through 389 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 382 through 389 current: chain 'M' and resid 441 through 447 Processing sheet with id=AD5, first strand: chain 'M' and resid 425 through 426 removed outlier: 3.670A pdb=" N THR M 431 " --> pdb=" O VAL M 426 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 32 through 33 removed outlier: 6.300A pdb=" N ILE N 5 " --> pdb=" O TRP N 33 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LYS N 4 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU N 61 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE N 6 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL N 63 " --> pdb=" O PHE N 6 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER N 8 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE N 95 " --> pdb=" O CYS N 58 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE N 60 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU N 97 " --> pdb=" O PHE N 60 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU N 62 " --> pdb=" O LEU N 97 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 164 through 165 Processing sheet with id=AD8, first strand: chain 'N' and resid 208 through 209 Processing sheet with id=AD9, first strand: chain 'N' and resid 283 through 286 996 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 58 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 11.20 Time building geometry restraints manager: 14.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9154 1.34 - 1.46: 7889 1.46 - 1.58: 15426 1.58 - 1.70: 319 1.70 - 1.82: 140 Bond restraints: 32928 Sorted by residual: bond pdb=" CB PRO M 378 " pdb=" CG PRO M 378 " ideal model delta sigma weight residual 1.492 1.666 -0.174 5.00e-02 4.00e+02 1.21e+01 bond pdb=" C2' U K 1 " pdb=" O2' U K 1 " ideal model delta sigma weight residual 1.412 1.381 0.031 1.50e-02 4.44e+03 4.19e+00 bond pdb=" C2' U C 1 " pdb=" O2' U C 1 " ideal model delta sigma weight residual 1.412 1.441 -0.029 1.50e-02 4.44e+03 3.76e+00 bond pdb=" CG1 ILE J 265 " pdb=" CD1 ILE J 265 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.05e+00 bond pdb=" CB GLU E 415 " pdb=" CG GLU E 415 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.78e+00 ... (remaining 32923 not shown) Histogram of bond angle deviations from ideal: 94.80 - 102.71: 294 102.71 - 110.62: 10360 110.62 - 118.53: 15838 118.53 - 126.44: 17694 126.44 - 134.35: 1042 Bond angle restraints: 45228 Sorted by residual: angle pdb=" CA PRO M 378 " pdb=" N PRO M 378 " pdb=" CD PRO M 378 " ideal model delta sigma weight residual 112.00 97.29 14.71 1.40e+00 5.10e-01 1.10e+02 angle pdb=" C3' U C 1 " pdb=" C2' U C 1 " pdb=" O2' U C 1 " ideal model delta sigma weight residual 114.60 106.38 8.22 1.50e+00 4.44e-01 3.00e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 125.85 -13.15 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CA GLU J 274 " pdb=" CB GLU J 274 " pdb=" CG GLU J 274 " ideal model delta sigma weight residual 114.10 122.35 -8.25 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CB ARG B 257 " pdb=" CG ARG B 257 " pdb=" CD ARG B 257 " ideal model delta sigma weight residual 111.30 120.60 -9.30 2.30e+00 1.89e-01 1.63e+01 ... (remaining 45223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 18175 33.89 - 67.78: 1284 67.78 - 101.66: 77 101.66 - 135.55: 1 135.55 - 169.44: 11 Dihedral angle restraints: 19548 sinusoidal: 9278 harmonic: 10270 Sorted by residual: dihedral pdb=" O4' U K 15 " pdb=" C1' U K 15 " pdb=" N1 U K 15 " pdb=" C2 U K 15 " ideal model delta sinusoidal sigma weight residual -160.00 9.44 -169.44 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U C 15 " pdb=" C1' U C 15 " pdb=" N1 U C 15 " pdb=" C2 U C 15 " ideal model delta sinusoidal sigma weight residual -160.00 6.92 -166.92 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U G 15 " pdb=" C1' U G 15 " pdb=" N1 U G 15 " pdb=" C2 U G 15 " ideal model delta sinusoidal sigma weight residual 200.00 44.25 155.75 1 1.50e+01 4.44e-03 8.16e+01 ... (remaining 19545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4304 0.060 - 0.119: 615 0.119 - 0.179: 53 0.179 - 0.238: 5 0.238 - 0.298: 3 Chirality restraints: 4980 Sorted by residual: chirality pdb=" C2' U C 1 " pdb=" C3' U C 1 " pdb=" O2' U C 1 " pdb=" C1' U C 1 " both_signs ideal model delta sigma weight residual False -2.52 -2.82 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CG LEU J 264 " pdb=" CB LEU J 264 " pdb=" CD1 LEU J 264 " pdb=" CD2 LEU J 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE N 323 " pdb=" CA ILE N 323 " pdb=" CG1 ILE N 323 " pdb=" CG2 ILE N 323 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4977 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 377 " -0.085 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO M 378 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO M 378 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 378 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 392 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.02e+00 pdb=" N PRO E 393 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 393 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 393 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 181 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO B 182 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " 0.034 5.00e-02 4.00e+02 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1649 2.72 - 3.26: 30702 3.26 - 3.81: 54655 3.81 - 4.35: 67581 4.35 - 4.90: 109555 Nonbonded interactions: 264142 Sorted by model distance: nonbonded pdb=" OH TYR J 221 " pdb=" O TYR J 233 " model vdw 2.173 2.440 nonbonded pdb=" OH TYR N 221 " pdb=" O TYR N 233 " model vdw 2.197 2.440 nonbonded pdb=" OE2 GLU J 281 " pdb=" OH TYR J 383 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR E 463 " pdb=" O ASP E 474 " model vdw 2.216 2.440 nonbonded pdb=" N GLU E 99 " pdb=" OE1 GLU E 99 " model vdw 2.218 2.520 ... (remaining 264137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 306 or (resid 307 and (name N or \ name CA or name C or name O or name CB )) or resid 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 321 or (resi \ d 322 and (name N or name CA or name C or name O or name CB )) or resid 323 thro \ ugh 399 or (resid 400 and (name N or name CA or name C or name O or name CB )) o \ r resid 401 through 506)) selection = (chain 'E' and (resid 1 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 257 or (resid 258 through 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) or re \ sid 310 through 321 or (resid 322 and (name N or name CA or name C or name O or \ name CB )) or resid 323 through 399 or (resid 400 and (name N or name CA or name \ C or name O or name CB )) or resid 401 through 506)) selection = (chain 'I' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 257 or (resid 258 through 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 306 \ or (resid 307 and (name N or name CA or name C or name O or name CB )) or resid \ 308 through 321 or (resid 322 and (name N or name CA or name C or name O or name \ CB )) or resid 323 through 399 or (resid 400 and (name N or name CA or name C o \ r name O or name CB )) or resid 401 through 506)) selection = (chain 'M' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or \ name CA or name C or name O or name CB )) or resid 138 through 257 or (resid 25 \ 8 through 260 and (name N or name CA or name C or name O or name CB )) or resid \ 261 through 308 or (resid 309 and (name N or name CA or name C or name O or name \ CB )) or resid 310 through 506)) } ncs_group { reference = (chain 'B' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 108 or (resid 109 and (name N or \ name CA or name C or name O or name CB )) or resid 110 through 125 or (resid 126 \ and (name N or name CA or name C or name O or name CB )) or resid 127 through 1 \ 64 or (resid 165 and (name N or name CA or name C or name O or name CB )) or res \ id 166 through 220 or (resid 221 and (name N or name CA or name C or name O or n \ ame CB )) or resid 222 through 316 or (resid 317 and (name N or name CA or name \ C or name O or name CB )) or resid 318 through 370 or (resid 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 415 or (resid 416 \ and (name N or name CA or name C or name O or name CB )) or resid 417 through 4 \ 18)) selection = (chain 'F' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 99 or (resid 100 and (name N or nam \ e CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 125 \ or (resid 126 and (name N or name CA or name C or name O or name CB )) or resid \ 127 through 147 or (resid 148 and (name N or name CA or name C or name O or name \ CB )) or resid 149 through 164 or (resid 165 and (name N or name CA or name C o \ r name O or name CB )) or resid 166 through 316 or (resid 317 and (name N or nam \ e CA or name C or name O or name CB )) or resid 318 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 415 \ or (resid 416 and (name N or name CA or name C or name O or name CB )) or resid \ 417 through 418)) selection = (chain 'J' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 147 or (resid 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 through 220 or (resid 221 \ and (name N or name CA or name C or name O or name CB )) or resid 222 through 3 \ 16 or (resid 317 and (name N or name CA or name C or name O or name CB )) or res \ id 318 through 370 or (resid 371 and (name N or name CA or name C or name O or n \ ame CB )) or resid 372 through 418)) selection = (chain 'N' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 125 or (resid 126 a \ nd (name N or name CA or name C or name O or name CB )) or resid 127 through 147 \ or (resid 148 and (name N or name CA or name C or name O or name CB )) or resid \ 149 through 164 or (resid 165 and (name N or name CA or name C or name O or nam \ e CB )) or resid 166 through 220 or (resid 221 and (name N or name CA or name C \ or name O or name CB )) or resid 222 through 415 or (resid 416 and (name N or na \ me CA or name C or name O or name CB )) or resid 417 through 418)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 8 through 27) selection = (chain 'L' and resid 8 through 27) } 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=0.01 max=1.00 mean=0.91 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.850 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 92.170 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 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 0.174 32928 Z= 0.204 Angle : 0.659 14.711 45228 Z= 0.345 Chirality : 0.042 0.298 4980 Planarity : 0.004 0.119 5118 Dihedral : 20.376 169.439 12908 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.90 % Favored : 93.07 % Rotamer: Outliers : 4.65 % Allowed : 29.35 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3464 helix: 0.84 (0.16), residues: 1132 sheet: -0.84 (0.21), residues: 590 loop : -1.83 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 219 HIS 0.007 0.001 HIS N 340 PHE 0.023 0.001 PHE N 17 TYR 0.020 0.001 TYR A 411 ARG 0.018 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 294 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 PHE cc_start: 0.8636 (m-80) cc_final: 0.8432 (m-10) REVERT: A 484 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7448 (OUTLIER) REVERT: B 167 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7351 (mtmm) REVERT: B 227 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8178 (mt) REVERT: F 309 MET cc_start: 0.5347 (tmm) cc_final: 0.5113 (tmm) REVERT: J 287 MET cc_start: 0.5705 (mmp) cc_final: 0.5466 (mmm) REVERT: M 399 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6651 (p) REVERT: N 223 PHE cc_start: 0.4722 (m-80) cc_final: 0.4418 (m-10) outliers start: 143 outliers final: 74 residues processed: 424 average time/residue: 1.2377 time to fit residues: 637.1867 Evaluate side-chains 249 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 172 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 470 CYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 303 MET Chi-restraints excluded: chain E residue 377 THR Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 413 ASN Chi-restraints excluded: chain F residue 414 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 219 ILE Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 232 ARG Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 387 THR Chi-restraints excluded: chain I residue 399 THR Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 498 THR Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 415 SER Chi-restraints excluded: chain M residue 41 SER Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 399 THR Chi-restraints excluded: chain M residue 422 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain M residue 486 ILE Chi-restraints excluded: chain M residue 498 THR Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 389 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 414 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.9980 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 323 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS B 116 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 HIS B 226 HIS E 217 HIS F 226 HIS I 66 ASN I 129 ASN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 GLN ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 ASN N 160 HIS ** N 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32928 Z= 0.192 Angle : 0.620 10.286 45228 Z= 0.325 Chirality : 0.042 0.291 4980 Planarity : 0.004 0.062 5118 Dihedral : 18.578 170.341 6021 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Rotamer: Outliers : 6.31 % Allowed : 26.88 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3464 helix: 1.15 (0.16), residues: 1158 sheet: -0.77 (0.22), residues: 608 loop : -1.69 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 219 HIS 0.013 0.001 HIS F 226 PHE 0.026 0.001 PHE A 304 TYR 0.014 0.001 TYR M 411 ARG 0.011 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 203 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 358 PHE cc_start: 0.8397 (m-80) cc_final: 0.8186 (m-80) REVERT: B 295 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6586 (mt) REVERT: B 388 ASP cc_start: 0.7543 (p0) cc_final: 0.7221 (p0) REVERT: I 273 ASP cc_start: 0.5764 (p0) cc_final: 0.5472 (p0) REVERT: J 352 ASP cc_start: 0.6341 (m-30) cc_final: 0.5588 (m-30) REVERT: M 399 THR cc_start: 0.6702 (OUTLIER) cc_final: 0.6135 (p) REVERT: N 223 PHE cc_start: 0.4734 (m-80) cc_final: 0.4442 (m-10) outliers start: 194 outliers final: 58 residues processed: 377 average time/residue: 1.1062 time to fit residues: 517.7067 Evaluate side-chains 222 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 161 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 301 GLU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 298 CYS Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 317 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 399 THR Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 160 HIS Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 chunk 321 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 259 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS B 160 HIS B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN F 358 HIS I 61 GLN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 GLN ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 GLN J 367 ASN M 66 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32928 Z= 0.329 Angle : 0.673 18.442 45228 Z= 0.349 Chirality : 0.043 0.315 4980 Planarity : 0.004 0.058 5118 Dihedral : 18.662 171.302 5947 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 6.05 % Allowed : 28.08 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3464 helix: 0.84 (0.15), residues: 1186 sheet: -0.86 (0.22), residues: 596 loop : -1.75 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 219 HIS 0.014 0.001 HIS N 160 PHE 0.024 0.002 PHE I 442 TYR 0.016 0.001 TYR A 411 ARG 0.013 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 166 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7620 (p0) REVERT: A 216 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7282 (ptpp) REVERT: B 388 ASP cc_start: 0.7621 (p0) cc_final: 0.7267 (p0) REVERT: F 309 MET cc_start: 0.5424 (tmm) cc_final: 0.5221 (tmm) REVERT: I 370 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7669 (t60) REVERT: J 279 ASP cc_start: 0.4942 (OUTLIER) cc_final: 0.4688 (p0) REVERT: J 352 ASP cc_start: 0.6322 (m-30) cc_final: 0.5556 (m-30) REVERT: N 289 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7237 (p0) outliers start: 186 outliers final: 77 residues processed: 334 average time/residue: 1.1546 time to fit residues: 478.6003 Evaluate side-chains 231 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 149 time to evaluate : 3.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 413 ASN Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 370 TRP Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain J residue 279 ASP Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 387 ASP Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 457 LYS Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 291 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 168 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 344 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS I 66 ASN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32928 Z= 0.341 Angle : 0.670 15.146 45228 Z= 0.348 Chirality : 0.043 0.334 4980 Planarity : 0.004 0.057 5118 Dihedral : 18.746 173.515 5938 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 6.93 % Allowed : 27.76 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3464 helix: 0.80 (0.15), residues: 1188 sheet: -0.90 (0.22), residues: 582 loop : -1.76 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 370 HIS 0.011 0.001 HIS E 207 PHE 0.015 0.002 PHE F 321 TYR 0.016 0.001 TYR I 150 ARG 0.008 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 155 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 216 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7367 (ptpp) REVERT: B 227 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8309 (mt) REVERT: B 388 ASP cc_start: 0.7649 (p0) cc_final: 0.7268 (p0) REVERT: E 213 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7700 (mtp180) REVERT: M 7 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7801 (mm) REVERT: M 468 ASN cc_start: 0.7847 (t0) cc_final: 0.7585 (t160) outliers start: 213 outliers final: 100 residues processed: 351 average time/residue: 1.1010 time to fit residues: 482.0412 Evaluate side-chains 245 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 140 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 387 ASP Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 457 LYS Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 15 ASN Chi-restraints excluded: chain N residue 16 ASP Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 291 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 HIS ** J 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 32928 Z= 0.405 Angle : 0.716 13.767 45228 Z= 0.370 Chirality : 0.045 0.356 4980 Planarity : 0.004 0.058 5118 Dihedral : 18.892 175.575 5938 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.94 % Favored : 91.95 % Rotamer: Outliers : 7.09 % Allowed : 27.86 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3464 helix: 0.61 (0.15), residues: 1188 sheet: -1.18 (0.21), residues: 610 loop : -1.82 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 370 HIS 0.009 0.001 HIS E 207 PHE 0.025 0.002 PHE A 304 TYR 0.019 0.001 TYR J 67 ARG 0.007 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 149 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7632 (p0) REVERT: A 216 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7346 (ptpp) REVERT: B 138 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: B 227 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 388 ASP cc_start: 0.7622 (p0) cc_final: 0.7293 (p0) REVERT: E 213 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7739 (mtp180) REVERT: E 215 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7945 (tp) REVERT: J 352 ASP cc_start: 0.6553 (m-30) cc_final: 0.5749 (m-30) REVERT: M 468 ASN cc_start: 0.7901 (t0) cc_final: 0.7639 (t160) REVERT: N 289 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7272 (p0) outliers start: 218 outliers final: 109 residues processed: 352 average time/residue: 1.1097 time to fit residues: 486.0991 Evaluate side-chains 253 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 137 time to evaluate : 3.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 291 THR Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 390 LYS Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 387 ASP Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 358 PHE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 457 LYS Chi-restraints excluded: chain M residue 460 LEU Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 15 ASN Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 289 ASN Chi-restraints excluded: chain N residue 315 LYS Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 0.7980 chunk 309 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 285 optimal weight: 0.0060 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 HIS ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32928 Z= 0.178 Angle : 0.655 16.083 45228 Z= 0.329 Chirality : 0.043 0.374 4980 Planarity : 0.003 0.056 5118 Dihedral : 18.774 179.368 5937 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 4.65 % Allowed : 30.23 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3464 helix: 1.01 (0.15), residues: 1194 sheet: -0.83 (0.22), residues: 604 loop : -1.74 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP I 370 HIS 0.012 0.001 HIS I 207 PHE 0.013 0.001 PHE N 223 TYR 0.014 0.001 TYR M 280 ARG 0.006 0.000 ARG N 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 173 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7602 (p0) REVERT: B 138 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: B 388 ASP cc_start: 0.7597 (p0) cc_final: 0.7305 (p0) REVERT: F 309 MET cc_start: 0.5100 (tmm) cc_final: 0.4874 (tmm) REVERT: J 352 ASP cc_start: 0.6558 (m-30) cc_final: 0.5758 (m-30) REVERT: J 395 MET cc_start: 0.2874 (pmm) cc_final: 0.2033 (ppp) outliers start: 143 outliers final: 69 residues processed: 301 average time/residue: 1.1227 time to fit residues: 422.1544 Evaluate side-chains 217 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 146 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 274 GLU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 384 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 315 LYS Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 251 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 289 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 343 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN M 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32928 Z= 0.350 Angle : 0.718 15.798 45228 Z= 0.363 Chirality : 0.044 0.370 4980 Planarity : 0.004 0.056 5118 Dihedral : 18.818 179.518 5928 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 4.62 % Allowed : 31.21 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3464 helix: 0.73 (0.15), residues: 1206 sheet: -0.83 (0.21), residues: 608 loop : -1.84 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 370 HIS 0.008 0.001 HIS I 207 PHE 0.033 0.002 PHE E 224 TYR 0.010 0.001 TYR M 425 ARG 0.012 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 144 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.7563 (p0) REVERT: B 138 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: E 213 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7645 (mtp180) REVERT: E 215 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7873 (tp) REVERT: E 471 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7573 (pp) REVERT: J 352 ASP cc_start: 0.6754 (m-30) cc_final: 0.5929 (m-30) REVERT: M 468 ASN cc_start: 0.7929 (t0) cc_final: 0.7675 (t160) REVERT: N 277 MET cc_start: 0.6695 (mmt) cc_final: 0.6454 (mpt) outliers start: 142 outliers final: 83 residues processed: 275 average time/residue: 1.0575 time to fit residues: 371.0933 Evaluate side-chains 222 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 134 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 213 ARG Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 405 ILE Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 274 VAL Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 387 ASP Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 143 VAL Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 358 PHE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 367 HIS Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 463 THR Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 34 CYS Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 269 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32928 Z= 0.183 Angle : 0.684 14.991 45228 Z= 0.340 Chirality : 0.043 0.366 4980 Planarity : 0.003 0.052 5118 Dihedral : 18.734 179.963 5927 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 3.87 % Allowed : 31.63 % Favored : 64.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3464 helix: 1.04 (0.16), residues: 1196 sheet: -0.75 (0.22), residues: 590 loop : -1.73 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 370 HIS 0.011 0.001 HIS I 207 PHE 0.017 0.001 PHE I 313 TYR 0.018 0.001 TYR M 411 ARG 0.009 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 163 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.7673 (p0) REVERT: B 142 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6883 (tptp) REVERT: B 388 ASP cc_start: 0.7512 (p0) cc_final: 0.7277 (p0) REVERT: E 460 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7518 (tm) REVERT: E 471 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7576 (pp) REVERT: I 16 HIS cc_start: 0.6303 (OUTLIER) cc_final: 0.5934 (m90) REVERT: J 352 ASP cc_start: 0.6784 (m-30) cc_final: 0.5946 (m-30) REVERT: J 395 MET cc_start: 0.3089 (pmm) cc_final: 0.1958 (tmt) REVERT: M 468 ASN cc_start: 0.7916 (t0) cc_final: 0.7662 (t160) REVERT: N 277 MET cc_start: 0.6727 (mmt) cc_final: 0.6451 (mpt) outliers start: 119 outliers final: 72 residues processed: 272 average time/residue: 1.0959 time to fit residues: 372.7204 Evaluate side-chains 221 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 144 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 395 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 HIS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 16 ASP Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 459 ILE Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 126 ARG Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 4.9990 chunk 328 optimal weight: 0.0870 chunk 299 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 98 optimal weight: 0.0000 chunk 288 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 318 optimal weight: 0.9980 overall best weight: 0.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32928 Z= 0.177 Angle : 0.694 14.007 45228 Z= 0.342 Chirality : 0.043 0.374 4980 Planarity : 0.003 0.061 5118 Dihedral : 18.669 175.652 5927 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.68 % Rotamer: Outliers : 3.12 % Allowed : 32.44 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3464 helix: 1.10 (0.16), residues: 1192 sheet: -0.72 (0.22), residues: 604 loop : -1.68 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 370 HIS 0.010 0.001 HIS I 207 PHE 0.030 0.001 PHE E 224 TYR 0.008 0.001 TYR J 213 ARG 0.014 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 161 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.7671 (p0) REVERT: B 142 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6913 (tptp) REVERT: B 165 ILE cc_start: 0.5877 (OUTLIER) cc_final: 0.5509 (pt) REVERT: B 268 LEU cc_start: 0.8452 (pp) cc_final: 0.8074 (pt) REVERT: B 388 ASP cc_start: 0.7509 (p0) cc_final: 0.7267 (p0) REVERT: E 460 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7629 (tm) REVERT: F 277 MET cc_start: 0.7464 (mmp) cc_final: 0.7157 (mmm) REVERT: J 395 MET cc_start: 0.3158 (pmm) cc_final: 0.2031 (tmt) REVERT: M 468 ASN cc_start: 0.7951 (t0) cc_final: 0.7720 (t160) REVERT: N 181 PHE cc_start: 0.6191 (p90) cc_final: 0.5983 (p90) outliers start: 96 outliers final: 69 residues processed: 248 average time/residue: 1.1686 time to fit residues: 360.9192 Evaluate side-chains 217 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 144 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 392 TYR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 126 ARG Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain N residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 5.9990 chunk 338 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 282 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 218 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 GLN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN M 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 32928 Z= 0.422 Angle : 0.772 13.806 45228 Z= 0.390 Chirality : 0.046 0.372 4980 Planarity : 0.004 0.065 5118 Dihedral : 18.803 178.700 5923 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.08 % Favored : 91.83 % Rotamer: Outliers : 3.22 % Allowed : 32.64 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.14), residues: 3464 helix: 0.65 (0.15), residues: 1206 sheet: -1.07 (0.21), residues: 630 loop : -1.80 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 370 HIS 0.007 0.001 HIS A 16 PHE 0.022 0.002 PHE A 304 TYR 0.030 0.001 TYR J 293 ARG 0.015 0.001 ARG J 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6928 Ramachandran restraints generated. 3464 Oldfield, 0 Emsley, 3464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 144 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7639 (p0) REVERT: B 165 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5756 (pt) REVERT: B 388 ASP cc_start: 0.7588 (p0) cc_final: 0.7339 (p0) REVERT: E 215 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7901 (tp) REVERT: E 471 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7513 (pp) REVERT: I 74 MET cc_start: 0.7003 (ppp) cc_final: 0.6749 (ppp) REVERT: J 395 MET cc_start: 0.3159 (pmm) cc_final: 0.1951 (tmt) REVERT: M 468 ASN cc_start: 0.8131 (t0) cc_final: 0.7891 (t160) REVERT: N 181 PHE cc_start: 0.6520 (p90) cc_final: 0.6300 (p90) REVERT: N 277 MET cc_start: 0.6551 (mmt) cc_final: 0.6282 (mpt) outliers start: 99 outliers final: 70 residues processed: 238 average time/residue: 1.0968 time to fit residues: 327.5037 Evaluate side-chains 211 residues out of total 3124 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 137 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 298 CYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 495 ASP Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 191 ASN Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 234 HIS Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 391 PHE Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 150 TYR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 463 THR Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 151 ASN Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain J residue 204 THR Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 318 ASN Chi-restraints excluded: chain J residue 391 PHE Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 403 VAL Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 103 LYS Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 215 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 348 GLU Chi-restraints excluded: chain M residue 350 ILE Chi-restraints excluded: chain M residue 365 PHE Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 405 ILE Chi-restraints excluded: chain M residue 423 VAL Chi-restraints excluded: chain M residue 470 CYS Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 239 ILE Chi-restraints excluded: chain N residue 380 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 0.8980 chunk 300 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 290 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 226 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** F 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.082496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.064130 restraints weight = 146254.712| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.97 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 355 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1004 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32928 Z= 0.193 Angle : 0.714 14.657 45228 Z= 0.353 Chirality : 0.043 0.381 4980 Planarity : 0.003 0.058 5118 Dihedral : 18.729 173.999 5923 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.32 % Favored : 93.62 % Rotamer: Outliers : 2.70 % Allowed : 33.16 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3464 helix: 0.99 (0.16), residues: 1196 sheet: -0.88 (0.23), residues: 584 loop : -1.66 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 370 HIS 0.011 0.001 HIS I 207 PHE 0.039 0.001 PHE A 304 TYR 0.008 0.001 TYR I 425 ARG 0.013 0.000 ARG J 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9278.28 seconds wall clock time: 169 minutes 24.47 seconds (10164.47 seconds total)