Starting phenix.real_space_refine on Fri Feb 6 20:19:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q8x_52912/02_2026/9q8x_52912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q8x_52912/02_2026/9q8x_52912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q8x_52912/02_2026/9q8x_52912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q8x_52912/02_2026/9q8x_52912.map" model { file = "/net/cci-nas-00/data/ceres_data/9q8x_52912/02_2026/9q8x_52912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q8x_52912/02_2026/9q8x_52912.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 298 5.49 5 S 71 5.16 5 C 16531 2.51 5 N 4846 2.21 5 O 5761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27507 Number of models: 1 Model: "" Number of chains: 14 Chain: "K" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3670 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 26, 'TRANS': 466} Chain breaks: 2 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 291 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 13, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'HIS:plan': 2, 'ARG:plan': 11, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 188 Chain: "L" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3874 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 26, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'ASP:plan': 9, 'GLN:plan1': 7, 'ASN:plan1': 2, 'HIS:plan': 4, 'GLU:plan': 17, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 228 Chain: "G" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 785 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 726 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 782 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "M" Number of atoms: 3844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3844 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 27, 'TRANS': 464} Chain breaks: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 2, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "N" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4080 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 620 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3075 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3069 Classifications: {'DNA': 149} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 148} Time building chain proxies: 6.04, per 1000 atoms: 0.22 Number of scatterers: 27507 At special positions: 0 Unit cell: (109.592, 146.672, 225.776, 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 71 16.00 P 298 15.00 O 5761 8.00 N 4846 7.00 C 16531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 961.9 milliseconds 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5314 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 27 sheets defined 45.4% alpha, 10.4% beta 67 base pairs and 231 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'K' and resid 58 through 77 Processing helix chain 'K' and resid 113 through 121 removed outlier: 3.746A pdb=" N LEU K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 132 Processing helix chain 'K' and resid 142 through 156 Processing helix chain 'K' and resid 182 through 196 removed outlier: 3.570A pdb=" N ALA K 186 " --> pdb=" O LYS K 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR K 188 " --> pdb=" O SER K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 250 Processing helix chain 'K' and resid 330 through 339 Processing helix chain 'K' and resid 354 through 356 No H-bonds generated for 'chain 'K' and resid 354 through 356' Processing helix chain 'K' and resid 377 through 393 Processing helix chain 'K' and resid 457 through 469 removed outlier: 4.589A pdb=" N LYS K 461 " --> pdb=" O GLU K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 495 Processing helix chain 'K' and resid 510 through 519 removed outlier: 3.543A pdb=" N MET K 514 " --> pdb=" O LYS K 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 530 Processing helix chain 'L' and resid 17 through 22 removed outlier: 3.813A pdb=" N ASN L 22 " --> pdb=" O PHE L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 48 removed outlier: 3.648A pdb=" N ALA L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 96 removed outlier: 3.892A pdb=" N LEU L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 120 removed outlier: 5.034A pdb=" N ILE L 112 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 157 removed outlier: 4.012A pdb=" N CYS L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 217 removed outlier: 3.557A pdb=" N LEU L 215 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU L 216 " --> pdb=" O MET L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 218 through 223 removed outlier: 4.369A pdb=" N LEU L 221 " --> pdb=" O GLU L 218 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP L 222 " --> pdb=" O ASP L 219 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU L 223 " --> pdb=" O GLY L 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 218 through 223' Processing helix chain 'L' and resid 227 through 233 Processing helix chain 'L' and resid 285 through 290 Processing helix chain 'L' and resid 324 through 332 removed outlier: 4.340A pdb=" N GLU L 329 " --> pdb=" O LYS L 325 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN L 330 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET L 331 " --> pdb=" O ASP L 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 349 through 351 No H-bonds generated for 'chain 'L' and resid 349 through 351' Processing helix chain 'L' and resid 352 through 356 removed outlier: 3.621A pdb=" N PHE L 356 " --> pdb=" O ARG L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 388 removed outlier: 4.273A pdb=" N ALA L 374 " --> pdb=" O ASP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 441 through 445 Processing helix chain 'L' and resid 448 through 461 Processing helix chain 'L' and resid 485 through 500 Processing helix chain 'L' and resid 509 through 517 Processing helix chain 'L' and resid 520 through 525 removed outlier: 3.699A pdb=" N LYS L 525 " --> pdb=" O GLU L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 527 through 536 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.308A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 97 Processing helix chain 'H' and resid 102 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.824A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.493A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 80 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'M' and resid 58 through 77 removed outlier: 3.906A pdb=" N SER M 77 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 120 Processing helix chain 'M' and resid 121 through 123 No H-bonds generated for 'chain 'M' and resid 121 through 123' Processing helix chain 'M' and resid 124 through 135 Processing helix chain 'M' and resid 142 through 157 removed outlier: 3.515A pdb=" N VAL M 146 " --> pdb=" O SER M 142 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 197 removed outlier: 3.844A pdb=" N ALA M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 removed outlier: 3.740A pdb=" N LEU M 242 " --> pdb=" O LYS M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 330 through 337 Processing helix chain 'M' and resid 354 through 356 No H-bonds generated for 'chain 'M' and resid 354 through 356' Processing helix chain 'M' and resid 377 through 393 removed outlier: 3.965A pdb=" N LEU M 381 " --> pdb=" O GLY M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 443 Processing helix chain 'M' and resid 459 through 469 Processing helix chain 'M' and resid 480 through 495 removed outlier: 4.045A pdb=" N LEU M 495 " --> pdb=" O GLU M 491 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 519 removed outlier: 3.636A pdb=" N GLY M 519 " --> pdb=" O ASN M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 527 removed outlier: 3.949A pdb=" N ASP M 523 " --> pdb=" O GLY M 519 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU M 527 " --> pdb=" O ASP M 523 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 removed outlier: 3.951A pdb=" N SER N 21 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 48 removed outlier: 4.185A pdb=" N GLN N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 73 removed outlier: 3.661A pdb=" N ASP N 72 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN N 73 " --> pdb=" O GLY N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 69 through 73' Processing helix chain 'N' and resid 87 through 97 removed outlier: 3.867A pdb=" N LEU N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 121 Processing helix chain 'N' and resid 143 through 146 removed outlier: 4.120A pdb=" N GLN N 146 " --> pdb=" O SER N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 143 through 146' Processing helix chain 'N' and resid 147 through 158 Processing helix chain 'N' and resid 198 through 214 Processing helix chain 'N' and resid 215 through 222 removed outlier: 7.748A pdb=" N GLU N 218 " --> pdb=" O LEU N 215 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP N 219 " --> pdb=" O GLU N 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP N 222 " --> pdb=" O ASP N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 232 removed outlier: 3.656A pdb=" N LEU N 231 " --> pdb=" O SER N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 331 removed outlier: 3.726A pdb=" N GLU N 329 " --> pdb=" O LYS N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 351 Processing helix chain 'N' and resid 352 through 356 Processing helix chain 'N' and resid 370 through 388 Processing helix chain 'N' and resid 426 through 430 removed outlier: 3.847A pdb=" N LEU N 430 " --> pdb=" O MET N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 461 Processing helix chain 'N' and resid 484 through 500 removed outlier: 4.264A pdb=" N GLN N 488 " --> pdb=" O ASN N 484 " (cutoff:3.500A) Processing helix chain 'N' and resid 509 through 517 removed outlier: 3.722A pdb=" N TRP N 513 " --> pdb=" O GLN N 509 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN N 517 " --> pdb=" O TRP N 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 519 through 525 removed outlier: 3.829A pdb=" N THR N 523 " --> pdb=" O PRO N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 526 through 536 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.658A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 removed outlier: 3.542A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.500A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.724A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.991A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 102 through 109 removed outlier: 6.683A pdb=" N VAL K 85 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU K 107 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU K 83 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER K 37 " --> pdb=" O ARG K 165 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N MET K 167 " --> pdb=" O SER K 37 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE K 39 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE K 169 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU K 41 " --> pdb=" O PHE K 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 259 through 261 removed outlier: 3.610A pdb=" N LEU K 259 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 271 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE K 269 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR K 369 " --> pdb=" O GLY K 272 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 432 " --> pdb=" O VAL K 368 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL K 394 " --> pdb=" O PRO K 415 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY K 349 " --> pdb=" O LEU K 397 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ARG K 399 " --> pdb=" O LEU K 347 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU K 347 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 319 through 322 removed outlier: 3.610A pdb=" N GLN K 320 " --> pdb=" O ILE K 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 375 through 376 removed outlier: 4.164A pdb=" N ILE L 540 " --> pdb=" O ILE K 376 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 79 through 84 removed outlier: 5.202A pdb=" N LEU L 83 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE L 54 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA L 55 " --> pdb=" O ALA L 8 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL L 10 " --> pdb=" O ALA L 55 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL L 57 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU L 12 " --> pdb=" O VAL L 57 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL L 11 " --> pdb=" O HIS L 131 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS L 13 " --> pdb=" O GLU L 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 164 through 165 removed outlier: 3.543A pdb=" N LEU L 165 " --> pdb=" O TYR L 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 249 through 251 removed outlier: 3.727A pdb=" N CYS L 249 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N GLN L 360 " --> pdb=" O GLN L 423 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN L 423 " --> pdb=" O GLN L 360 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR L 421 " --> pdb=" O LEU L 362 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS L 418 " --> pdb=" O HIS L 411 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 313 through 316 Processing sheet with id=AA9, first strand: chain 'L' and resid 342 through 347 removed outlier: 6.501A pdb=" N ILE L 392 " --> pdb=" O LEU L 343 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE L 345 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL L 390 " --> pdb=" O PHE L 345 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY L 406 " --> pdb=" O VAL L 393 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 464 through 466 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.419A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'G' and resid 100 through 102 removed outlier: 6.492A pdb=" N THR G 101 " --> pdb=" O TYR B 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.216A pdb=" N ARG E 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.158A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.545A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'M' and resid 103 through 104 removed outlier: 3.867A pdb=" N TYR M 103 " --> pdb=" O PHE M 87 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N VAL M 86 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE M 40 " --> pdb=" O VAL M 86 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG M 35 " --> pdb=" O MET M 161 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N HIS M 163 " --> pdb=" O ARG M 35 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG M 165 " --> pdb=" O SER M 37 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE M 39 " --> pdb=" O ARG M 165 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET M 167 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 261 through 262 removed outlier: 7.654A pdb=" N LEU M 347 " --> pdb=" O ARG M 399 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ARG M 399 " --> pdb=" O LEU M 347 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY M 349 " --> pdb=" O LEU M 397 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR M 400 " --> pdb=" O TYR M 409 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR M 409 " --> pdb=" O TYR M 400 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA M 412 " --> pdb=" O VAL M 435 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL M 435 " --> pdb=" O ALA M 412 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 287 through 289 Processing sheet with id=AC4, first strand: chain 'M' and resid 318 through 319 Processing sheet with id=AC5, first strand: chain 'N' and resid 78 through 84 removed outlier: 5.941A pdb=" N HIS N 80 " --> pdb=" O LEU N 58 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU N 58 " --> pdb=" O HIS N 80 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N HIS N 82 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU N 56 " --> pdb=" O HIS N 82 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL N 10 " --> pdb=" O ALA N 55 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL N 57 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU N 12 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA N 9 " --> pdb=" O HIS N 131 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU N 133 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL N 11 " --> pdb=" O GLU N 133 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE N 135 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS N 13 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG N 130 " --> pdb=" O SER N 160 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLN N 162 " --> pdb=" O ARG N 130 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE N 132 " --> pdb=" O GLN N 162 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE N 164 " --> pdb=" O ILE N 132 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE N 134 " --> pdb=" O PHE N 164 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N TYR N 225 " --> pdb=" O LEU N 161 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE N 163 " --> pdb=" O TYR N 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 250 through 253 removed outlier: 3.523A pdb=" N ILE N 259 " --> pdb=" O LEU N 251 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL N 361 " --> pdb=" O SER N 266 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASN N 359 " --> pdb=" O TYR N 421 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N TYR N 421 " --> pdb=" O ASN N 359 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N VAL N 361 " --> pdb=" O LEU N 419 " (cutoff:3.500A) removed outlier: 10.485A pdb=" N LEU N 419 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL N 422 " --> pdb=" O VAL N 407 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN N 404 " --> pdb=" O TYR N 395 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE N 392 " --> pdb=" O LEU N 343 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG N 250 " --> pdb=" O PHE N 340 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL N 342 " --> pdb=" O ARG N 250 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N THR N 252 " --> pdb=" O VAL N 342 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY N 344 " --> pdb=" O THR N 252 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 464 through 467 Processing sheet with id=AC8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.926A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 118 through 119 954 hydrogen bonds defined for protein. 2757 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 162 hydrogen bonds 316 hydrogen bond angles 0 basepair planarities 67 basepair parallelities 231 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7618 1.34 - 1.46: 6302 1.46 - 1.58: 14002 1.58 - 1.70: 596 1.70 - 1.82: 112 Bond restraints: 28630 Sorted by residual: bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" C3' DG J 77 " pdb=" O3' DG J 77 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" CG1 ILE C 62 " pdb=" CD1 ILE C 62 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.97e+00 bond pdb=" CB GLN L 432 " pdb=" CG GLN L 432 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" CG MET K 462 " pdb=" SD MET K 462 " ideal model delta sigma weight residual 1.803 1.772 0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 28625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 39636 2.26 - 4.52: 382 4.52 - 6.79: 40 6.79 - 9.05: 16 9.05 - 11.31: 6 Bond angle restraints: 40080 Sorted by residual: angle pdb=" C GLU K 250 " pdb=" N THR K 251 " pdb=" CA THR K 251 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" CA ILE L 528 " pdb=" CB ILE L 528 " pdb=" CG1 ILE L 528 " ideal model delta sigma weight residual 110.40 117.15 -6.75 1.70e+00 3.46e-01 1.57e+01 angle pdb=" CA MET L 357 " pdb=" CB MET L 357 " pdb=" CG MET L 357 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.45e+01 angle pdb=" C ARG G 17 " pdb=" N SER G 18 " pdb=" CA SER G 18 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" CA MET L 515 " pdb=" CB MET L 515 " pdb=" CG MET L 515 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.14e+01 ... (remaining 40075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 14319 31.82 - 63.65: 2120 63.65 - 95.47: 116 95.47 - 127.30: 2 127.30 - 159.12: 4 Dihedral angle restraints: 16561 sinusoidal: 8389 harmonic: 8172 Sorted by residual: dihedral pdb=" CA LEU H 99 " pdb=" C LEU H 99 " pdb=" N PRO H 100 " pdb=" CA PRO H 100 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ASN L 514 " pdb=" C ASN L 514 " pdb=" N MET L 515 " pdb=" CA MET L 515 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLU H 102 " pdb=" C GLU H 102 " pdb=" N LEU H 103 " pdb=" CA LEU H 103 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 16558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3659 0.044 - 0.087: 761 0.087 - 0.131: 195 0.131 - 0.175: 15 0.175 - 0.219: 3 Chirality restraints: 4633 Sorted by residual: chirality pdb=" CB ILE L 253 " pdb=" CA ILE L 253 " pdb=" CG1 ILE L 253 " pdb=" CG2 ILE L 253 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CG LEU G 116 " pdb=" CB LEU G 116 " pdb=" CD1 LEU G 116 " pdb=" CD2 LEU G 116 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE N 392 " pdb=" CA ILE N 392 " pdb=" CG1 ILE N 392 " pdb=" CG2 ILE N 392 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 4630 not shown) Planarity restraints: 4107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 513 " 0.035 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP N 513 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP N 513 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP N 513 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP N 513 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP N 513 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP N 513 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 513 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 513 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP N 513 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 431 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C ARG L 431 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG L 431 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN L 432 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR M 58 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO M 59 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO M 59 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO M 59 " 0.029 5.00e-02 4.00e+02 ... (remaining 4104 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 12066 2.96 - 3.44: 27839 3.44 - 3.93: 48550 3.93 - 4.41: 56164 4.41 - 4.90: 81855 Nonbonded interactions: 226474 Sorted by model distance: nonbonded pdb=" O5' DA J 119 " pdb=" O4' DA J 119 " model vdw 2.471 2.432 nonbonded pdb=" O5' DT J 146 " pdb=" O4' DT J 146 " model vdw 2.473 2.432 nonbonded pdb=" O5' DG J 77 " pdb=" O4' DG J 77 " model vdw 2.489 2.432 nonbonded pdb=" O5' DC J 137 " pdb=" O4' DC J 137 " model vdw 2.493 2.432 nonbonded pdb=" O5' DA J 6 " pdb=" O4' DA J 6 " model vdw 2.512 2.432 ... (remaining 226469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 39 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 133)) selection = (chain 'E' and resid 39 through 133) } ncs_group { reference = (chain 'B' and (resid 23 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 100)) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 70 or (resid 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 through 87 or (re \ sid 88 and (name N or name CA or name C or name O or name CB )) or resid 89 thro \ ugh 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or \ resid 92 through 116)) selection = (chain 'G' and resid 13 through 116) } ncs_group { reference = (chain 'D' and ((resid 26 through 27 and (name N or name CA or name C or name O \ or name CB )) or resid 28 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 42 or (resid 43 and (name N or na \ me CA or name C or name O or name CB )) or resid 44 through 101 or (resid 102 an \ d (name N or name CA or name C or name O or name CB )) or resid 103 through 104 \ or (resid 105 and (name N or name CA or name C or name O or name CB )) or resid \ 106 through 116 or (resid 117 and (name N or name CA or name C or name O or name \ CB )) or resid 118 through 121)) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 34 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 102 or (resid 103 and \ (name N or name CA or name C or name O or name CB )) or resid 104 through 122 o \ r (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 24 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 or (resid 137 and (name N or name CA or name C or name O or n \ ame CB )) or resid 138 through 163 or (resid 164 and (name N or name CA or name \ C or name O or name CB )) or resid 165 through 166 or (resid 167 and (name N or \ name CA or name C or name O or name CB )) or resid 168 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 2 \ 22 or (resid 231 through 232 and (name N or name CA or name C or name O or name \ CB )) or resid 233 through 242 or (resid 243 and (name N or name CA or name C or \ name O or name CB )) or resid 244 through 281 or (resid 282 and (name N or name \ CA or name C or name O or name CB )) or resid 283 through 288 or (resid 289 thr \ ough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 325 or resid 327 through 352 or (resid 353 and (name N or name CA or name \ C or name O or name CB )) or resid 354 or (resid 355 and (name N or name CA or \ name C or name O or name CB )) or resid 356 through 362 or (resid 363 and (name \ N or name CA or name C or name O or name CB )) or resid 364 through 390 or (resi \ d 391 and (name N or name CA or name C or name O or name CB )) or resid 392 thro \ ugh 434 or (resid 435 and (name N or name CA or name C or name O or name CB )) o \ r resid 436 through 511 or (resid 512 through 513 and (name N or name CA or name \ C or name O or name CB )) or resid 514 through 529 or (resid 530 and (name N or \ name CA or name C or name O or name CB )) or resid 531 through 534)) selection = (chain 'M' and (resid 34 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 55 or (res \ id 56 through 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 90 or (resid 91 through 92 and (name N or name CA or name C or nam \ e O or name CB )) or resid 93 through 96 or (resid 97 through 98 and (name N or \ name CA or name C or name O or name CB )) or resid 99 or (resid 100 and (name N \ or name CA or name C or name O or name CB )) or resid 101 through 106 or (resid \ 107 and (name N or name CA or name C or name O or name CB )) or resid 108 throug \ h 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) or \ resid 115 through 116 or (resid 117 through 118 and (name N or name CA or name C \ or name O or name CB )) or resid 119 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 132 or resid 134 t \ hrough 144 or (resid 145 and (name N or name CA or name C or name O or name CB ) \ ) or resid 146 through 147 or (resid 148 and (name N or name CA or name C or nam \ e O or name CB )) or resid 149 through 155 or (resid 156 and (name N or name CA \ or name C or name O or name CB )) or resid 157 or (resid 158 and (name N or name \ CA or name C or name O or name CB )) or resid 159 or (resid 160 through 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 175 o \ r (resid 176 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 77 through 181 or (resid 182 through 183 and (name N or name CA or name C or nam \ e O or name CB )) or resid 184 or (resid 185 through 187 and (name N or name CA \ or name C or name O or name CB )) or resid 188 through 193 or (resid 194 through \ 195 and (name N or name CA or name C or name O or name CB )) or resid 196 throu \ gh 213 or (resid 214 through 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 233 or (resid 234 and (name N or name CA or name \ C or name O or name CB )) or resid 235 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 246 or (resid 247 \ through 248 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 49 through 252 or (resid 253 and (name N or name CA or name C or name O or name \ CB )) or resid 254 through 257 or (resid 258 and (name N or name CA or name C or \ name O or name CB )) or resid 259 through 265 or (resid 266 and (name N or name \ CA or name C or name O or name CB )) or resid 267 through 289 or (resid 290 and \ (name N or name CA or name C or name O or name CB )) or resid 291 through 293 o \ r (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 95 through 296 or (resid 297 through 299 and (name N or name CA or name C or nam \ e O or name CB )) or resid 300 or (resid 301 and (name N or name CA or name C or \ name O or name CB )) or resid 302 through 306 or resid 314 through 317 or (resi \ d 318 and (name N or name CA or name C or name O or name CB )) or resid 319 thro \ ugh 331 or (resid 332 and (name N or name CA or name C or name O or name CB )) o \ r resid 333 through 356 or (resid 357 through 358 and (name N or name CA or name \ C or name O or name CB )) or resid 359 through 421 or (resid 422 and (name N or \ name CA or name C or name O or name CB )) or resid 423 through 443 or (resid 44 \ 4 through 446 and (name N or name CA or name C or name O or name CB )) or resid \ 447 or (resid 448 through 450 and (name N or name CA or name C or name O or name \ CB )) or resid 451 through 457 or (resid 458 and (name N or name CA or name C o \ r name O or name CB )) or resid 459 through 462 or (resid 463 through 465 and (n \ ame N or name CA or name C or name O or name CB )) or resid 466 or (resid 467 th \ rough 468 and (name N or name CA or name C or name O or name CB )) or resid 469 \ or (resid 470 and (name N or name CA or name C or name O or name CB )) or resid \ 471 through 473 or (resid 474 and (name N or name CA or name C or name O or name \ CB )) or resid 475 through 477 or (resid 478 and (name N or name CA or name C o \ r name O or name CB )) or resid 479 through 495 or (resid 496 and (name N or nam \ e CA or name C or name O or name CB )) or resid 497 through 500 or (resid 501 an \ d (name N or name CA or name C or name O or name CB )) or resid 502 through 509 \ or (resid 510 and (name N or name CA or name C or name O or name CB )) or resid \ 511 through 519 or (resid 520 and (name N or name CA or name C or name O or name \ CB )) or resid 521 through 525 or (resid 526 through 527 and (name N or name CA \ or name C or name O or name CB )) or resid 528 through 533 or (resid 534 and (n \ ame N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'L' and (resid 6 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 31 or (resid 32 and (name N or name \ CA or name C or name O or name CB )) or resid 33 through 39 or (resid 40 and (n \ ame N or name CA or name C or name O or name CB )) or resid 41 through 46 or (re \ sid 47 through 48 and (name N or name CA or name C or name O or name CB )) or re \ sid 49 through 81 or (resid 82 and (name N or name CA or name C or name O or nam \ e CB )) or resid 83 or (resid 84 and (name N or name CA or name C or name O or n \ ame CB )) or resid 85 through 106 or (resid 107 and (name N or name CA or name C \ or name O or name CB )) or resid 108 through 122 or (resid 123 and (name N or n \ ame CA or name C or name O or name CB )) or resid 124 through 208 or (resid 209 \ through 210 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 1 through 235 or (resid 236 and (name N or name CA or name C or name O or name C \ B )) or resid 237 through 245 or (resid 246 and (name N or name CA or name C or \ name O or name CB )) or resid 247 through 259 or (resid 260 and (name N or name \ CA or name C or name O or name CB )) or resid 261 through 283 or (resid 284 thro \ ugh 287 and (name N or name CA or name C or name O or name CB )) or resid 288 th \ rough 310 or (resid 311 through 312 and (name N or name CA or name C or name O o \ r name CB )) or resid 313 through 330 or (resid 331 and (name N or name CA or na \ me C or name O or name CB )) or resid 332 through 359 or (resid 360 and (name N \ or name CA or name C or name O or name CB )) or resid 361 through 362 or (resid \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throug \ h 397 or (resid 398 and (name N or name CA or name C or name O or name CB )) or \ resid 399 through 403 or (resid 404 and (name N or name CA or name C or name O o \ r name CB )) or resid 405 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 412 or (resid 413 through 414 \ and (name N or name CA or name C or name O or name CB )) or resid 415 through 42 \ 6 or (resid 427 through 428 and (name N or name CA or name C or name O or name C \ B )) or resid 429 through 499 or (resid 500 and (name N or name CA or name C or \ name O or name CB )) or resid 501 through 543)) selection = (chain 'N' and (resid 6 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 64 or (resid 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 67 or (re \ sid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 thro \ ugh 72 or (resid 73 and (name N or name CA or name C or name O or name CB )) or \ resid 74 through 88 or (resid 89 and (name N or name CA or name C or name O or n \ ame CB )) or resid 90 through 96 or (resid 97 and (name N or name CA or name C o \ r name O or name CB )) or resid 98 through 120 or (resid 121 and (name N or name \ CA or name C or name O or name CB )) or resid 122 through 125 or (resid 126 and \ (name N or name CA or name C or name O or name CB )) or resid 127 or (resid 128 \ through 131 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 32 through 140 or (resid 141 through 142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 143 or (resid 144 and (name N or name CA or name C or \ name O or name CB )) or resid 145 through 147 or (resid 148 and (name N or name \ CA or name C or name O or name CB )) or resid 149 through 154 or (resid 155 thr \ ough 156 and (name N or name CA or name C or name O or name CB )) or resid 157 t \ hrough 160 or (resid 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 through 183 or (resid 184 and (name N or name CA or name C or nam \ e O or name CB )) or resid 185 through 191 or (resid 192 and (name N or name CA \ or name C or name O or name CB )) or resid 193 through 198 or (resid 199 through \ 200 and (name N or name CA or name C or name O or name CB )) or resid 201 or (r \ esid 202 through 203 and (name N or name CA or name C or name O or name CB )) or \ resid 204 through 218 or (resid 219 and (name N or name CA or name C or name O \ or name CB )) or resid 220 through 237 or (resid 238 through 239 and (name N or \ name CA or name C or name O or name CB )) or resid 240 through 249 or (resid 250 \ and (name N or name CA or name C or name O or name CB )) or resid 251 or (resid \ 252 and (name N or name CA or name C or name O or name CB )) or resid 253 throu \ gh 255 or (resid 256 and (name N or name CA or name C or name O or name CB )) or \ resid 257 through 269 or (resid 270 and (name N or name CA or name C or name O \ or name CB )) or resid 271 through 273 or (resid 274 and (name N or name CA or n \ ame C or name O or name CB )) or resid 275 through 281 or (resid 282 and (name N \ or name CA or name C or name O or name CB )) or resid 283 through 291 or (resid \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 throu \ gh 294 or (resid 295 and (name N or name CA or name C or name O or name CB )) or \ resid 296 through 299 or (resid 300 and (name N or name CA or name C or name O \ or name CB )) or resid 301 or (resid 302 and (name N or name CA or name C or nam \ e O or name CB )) or resid 303 or (resid 304 and (name N or name CA or name C or \ name O or name CB )) or resid 305 through 306 or (resid 307 through 308 and (na \ me N or name CA or name C or name O or name CB )) or resid 309 through 311 or (r \ esid 312 and (name N or name CA or name C or name O or name CB )) or resid 313 t \ hrough 317 or (resid 318 and (name N or name CA or name C or name O or name CB ) \ ) or resid 319 through 324 or (resid 325 and (name N or name CA or name C or nam \ e O or name CB )) or resid 326 or (resid 327 and (name N or name CA or name C or \ name O or name CB )) or resid 328 or (resid 329 through 331 and (name N or name \ CA or name C or name O or name CB )) or resid 332 through 333 or (resid 334 and \ (name N or name CA or name C or name O or name CB )) or resid 335 through 351 o \ r (resid 352 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 53 or (resid 354 and (name N or name CA or name C or name O or name CB )) or res \ id 355 through 367 or (resid 368 through 374 and (name N or name CA or name C or \ name O or name CB )) or resid 375 through 388 or (resid 389 and (name N or name \ CA or name C or name O or name CB )) or resid 390 through 399 or (resid 400 thr \ ough 401 and (name N or name CA or name C or name O or name CB )) or resid 402 t \ hrough 413 or (resid 414 and (name N or name CA or name C or name O or name CB ) \ ) or resid 415 through 423 or (resid 424 and (name N or name CA or name C or nam \ e O or name CB )) or resid 425 through 427 or (resid 428 and (name N or name CA \ or name C or name O or name CB )) or resid 429 through 433 or (resid 434 and (na \ me N or name CA or name C or name O or name CB )) or resid 435 through 447 or (r \ esid 448 through 449 and (name N or name CA or name C or name O or name CB )) or \ resid 450 through 465 or (resid 466 and (name N or name CA or name C or name O \ or name CB )) or resid 467 or (resid 468 through 471 and (name N or name CA or n \ ame C or name O or name CB )) or resid 472 through 473 or (resid 474 and (name N \ or name CA or name C or name O or name CB )) or resid 475 through 491 or (resid \ 492 and (name N or name CA or name C or name O or name CB )) or resid 493 throu \ gh 504 or (resid 505 and (name N or name CA or name C or name O or name CB )) or \ resid 506 through 512 or (resid 513 and (name N or name CA or name C or name O \ or name CB )) or resid 514 through 540 or (resid 541 through 543 and (name N or \ name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 9.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.440 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.070 28630 Z= 0.146 Angle : 0.601 11.310 40080 Z= 0.323 Chirality : 0.038 0.219 4633 Planarity : 0.004 0.059 4107 Dihedral : 24.478 159.123 11247 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.13 % Rotamer: Outliers : 0.54 % Allowed : 29.32 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2761 helix: 1.28 (0.16), residues: 1149 sheet: -1.70 (0.29), residues: 314 loop : -1.63 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 431 TYR 0.018 0.001 TYR H 39 PHE 0.018 0.001 PHE D 62 TRP 0.067 0.003 TRP N 513 HIS 0.011 0.001 HIS L 511 Details of bonding type rmsd covalent geometry : bond 0.00321 (28630) covalent geometry : angle 0.60090 (40080) hydrogen bonds : bond 0.16221 ( 1116) hydrogen bonds : angle 7.82174 ( 3073) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: K 135 MET cc_start: 0.4444 (tpp) cc_final: 0.2425 (mpp) REVERT: K 348 MET cc_start: 0.1965 (mtp) cc_final: 0.0189 (ttt) REVERT: K 499 GLU cc_start: 0.5954 (mp0) cc_final: 0.5231 (tt0) REVERT: L 461 MET cc_start: 0.2982 (tpt) cc_final: 0.2555 (tpp) REVERT: H 32 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6086 (tp30) REVERT: C 95 LYS cc_start: 0.9442 (tptm) cc_final: 0.8991 (ttmt) REVERT: M 91 GLU cc_start: 0.2954 (mp0) cc_final: 0.2200 (tm-30) REVERT: M 133 ASP cc_start: 0.1752 (t0) cc_final: 0.1509 (p0) REVERT: A 129 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7834 (tmm160) outliers start: 12 outliers final: 3 residues processed: 139 average time/residue: 0.7753 time to fit residues: 123.7300 Evaluate side-chains 123 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 416 GLN K 433 GLN ** L 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 HIS N 411 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.158457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.098794 restraints weight = 73912.862| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.86 r_work: 0.3219 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28630 Z= 0.192 Angle : 0.592 11.995 40080 Z= 0.321 Chirality : 0.040 0.188 4633 Planarity : 0.004 0.055 4107 Dihedral : 25.946 158.555 6281 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.31 % Rotamer: Outliers : 2.57 % Allowed : 27.47 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2761 helix: 1.35 (0.16), residues: 1180 sheet: -1.47 (0.30), residues: 292 loop : -1.65 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 404 TYR 0.016 0.001 TYR H 39 PHE 0.011 0.001 PHE K 87 TRP 0.028 0.002 TRP N 513 HIS 0.010 0.001 HIS L 511 Details of bonding type rmsd covalent geometry : bond 0.00437 (28630) covalent geometry : angle 0.59154 (40080) hydrogen bonds : bond 0.04678 ( 1116) hydrogen bonds : angle 4.99285 ( 3073) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 0.905 Fit side-chains REVERT: K 135 MET cc_start: 0.4654 (tpp) cc_final: 0.3143 (mpt) REVERT: K 348 MET cc_start: 0.2101 (mtp) cc_final: 0.0727 (ttt) REVERT: K 499 GLU cc_start: 0.6038 (mp0) cc_final: 0.5285 (tt0) REVERT: L 432 GLN cc_start: 0.3043 (OUTLIER) cc_final: 0.1232 (pp30) REVERT: L 461 MET cc_start: 0.3009 (tpt) cc_final: 0.2567 (tpp) REVERT: G 38 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.6787 (p90) REVERT: G 92 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8679 (mt-10) REVERT: E 129 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8577 (tmt170) REVERT: E 133 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: C 95 LYS cc_start: 0.9537 (tptm) cc_final: 0.9072 (ttmt) REVERT: M 91 GLU cc_start: 0.3089 (mp0) cc_final: 0.2578 (tm-30) REVERT: M 133 ASP cc_start: 0.1710 (t0) cc_final: 0.1492 (p0) REVERT: M 386 LEU cc_start: -0.2699 (OUTLIER) cc_final: -0.3166 (pp) REVERT: A 129 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.7960 (tmm160) outliers start: 57 outliers final: 13 residues processed: 168 average time/residue: 0.7141 time to fit residues: 138.3636 Evaluate side-chains 135 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain G residue 29 ARG Chi-restraints excluded: chain G residue 38 HIS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain N residue 381 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 66 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.0270 chunk 267 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 GLN ** L 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 HIS H 81 ASN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.155647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.095027 restraints weight = 73055.206| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 6.15 r_work: 0.3078 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 28630 Z= 0.366 Angle : 0.682 10.478 40080 Z= 0.368 Chirality : 0.047 0.224 4633 Planarity : 0.005 0.085 4107 Dihedral : 26.517 158.219 6278 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.19 % Favored : 93.70 % Rotamer: Outliers : 3.52 % Allowed : 27.56 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2761 helix: 1.03 (0.15), residues: 1186 sheet: -1.54 (0.30), residues: 288 loop : -1.69 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 20 TYR 0.030 0.002 TYR H 39 PHE 0.014 0.002 PHE H 67 TRP 0.023 0.002 TRP N 513 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00849 (28630) covalent geometry : angle 0.68214 (40080) hydrogen bonds : bond 0.05402 ( 1116) hydrogen bonds : angle 4.94185 ( 3073) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 112 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: K 105 LEU cc_start: 0.1218 (OUTLIER) cc_final: 0.0726 (tt) REVERT: K 135 MET cc_start: 0.4688 (tpp) cc_final: 0.3325 (mpp) REVERT: K 348 MET cc_start: 0.1587 (mtp) cc_final: 0.0383 (ttt) REVERT: K 499 GLU cc_start: 0.6060 (mp0) cc_final: 0.5298 (tt0) REVERT: L 432 GLN cc_start: 0.2900 (OUTLIER) cc_final: 0.0967 (pp30) REVERT: L 461 MET cc_start: 0.2995 (OUTLIER) cc_final: 0.2596 (tpp) REVERT: G 17 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8656 (mtp180) REVERT: H 30 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8150 (mtm180) REVERT: E 97 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8715 (mp0) REVERT: E 129 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8795 (tmt170) REVERT: C 95 LYS cc_start: 0.9563 (tptm) cc_final: 0.9060 (ttmt) REVERT: M 91 GLU cc_start: 0.3034 (mp0) cc_final: 0.2667 (tm-30) REVERT: M 133 ASP cc_start: 0.1751 (t0) cc_final: 0.1537 (p0) REVERT: M 386 LEU cc_start: -0.2717 (OUTLIER) cc_final: -0.3281 (pp) REVERT: A 129 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.7811 (tmm160) outliers start: 78 outliers final: 19 residues processed: 174 average time/residue: 0.6674 time to fit residues: 135.1085 Evaluate side-chains 141 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain M residue 203 MET Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain M residue 504 VAL Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 381 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 86 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 34 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 296 optimal weight: 0.8980 chunk 163 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 223 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 HIS ** L 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 HIS ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN M 458 GLN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 411 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.157913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.098693 restraints weight = 73071.715| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 5.47 r_work: 0.3209 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28630 Z= 0.154 Angle : 0.563 9.508 40080 Z= 0.307 Chirality : 0.038 0.191 4633 Planarity : 0.004 0.056 4107 Dihedral : 26.201 160.140 6278 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.36 % Favored : 94.53 % Rotamer: Outliers : 2.93 % Allowed : 28.64 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2761 helix: 1.36 (0.15), residues: 1184 sheet: -1.42 (0.30), residues: 293 loop : -1.61 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 26 TYR 0.015 0.001 TYR H 39 PHE 0.014 0.001 PHE M 131 TRP 0.024 0.001 TRP N 513 HIS 0.021 0.001 HIS L 246 Details of bonding type rmsd covalent geometry : bond 0.00346 (28630) covalent geometry : angle 0.56325 (40080) hydrogen bonds : bond 0.03753 ( 1116) hydrogen bonds : angle 4.53569 ( 3073) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 124 time to evaluate : 0.899 Fit side-chains REVERT: K 132 GLN cc_start: 0.5201 (OUTLIER) cc_final: 0.4922 (mm-40) REVERT: K 135 MET cc_start: 0.4338 (tpp) cc_final: 0.3036 (mpp) REVERT: K 348 MET cc_start: 0.2061 (mtp) cc_final: 0.0753 (ttt) REVERT: K 499 GLU cc_start: 0.6068 (mp0) cc_final: 0.5310 (tt0) REVERT: L 247 TRP cc_start: 0.7057 (t60) cc_final: 0.6373 (t60) REVERT: L 432 GLN cc_start: 0.3101 (OUTLIER) cc_final: 0.1330 (pp30) REVERT: L 461 MET cc_start: 0.2977 (OUTLIER) cc_final: 0.2343 (mmm) REVERT: E 133 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: C 95 LYS cc_start: 0.9507 (tptm) cc_final: 0.9058 (ttmt) REVERT: M 91 GLU cc_start: 0.3039 (mp0) cc_final: 0.2464 (tm-30) REVERT: M 133 ASP cc_start: 0.1781 (t0) cc_final: 0.1539 (p0) REVERT: M 517 ARG cc_start: 0.2274 (OUTLIER) cc_final: 0.1985 (ptm160) REVERT: A 129 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7976 (tmm160) outliers start: 65 outliers final: 18 residues processed: 173 average time/residue: 0.6693 time to fit residues: 135.5821 Evaluate side-chains 139 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 188 HIS Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 203 MET Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 0 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 150 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 11 optimal weight: 40.0000 chunk 235 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 502 GLN L 80 HIS ** L 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 HIS ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN D 81 ASN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.153469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.090612 restraints weight = 72902.244| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 5.47 r_work: 0.3034 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.126 28630 Z= 0.591 Angle : 0.815 11.766 40080 Z= 0.438 Chirality : 0.058 0.408 4633 Planarity : 0.006 0.069 4107 Dihedral : 26.828 158.935 6278 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.39 % Favored : 92.50 % Rotamer: Outliers : 4.33 % Allowed : 28.01 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2761 helix: 0.69 (0.15), residues: 1184 sheet: -1.60 (0.30), residues: 292 loop : -1.81 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 17 TYR 0.034 0.002 TYR H 39 PHE 0.023 0.002 PHE H 67 TRP 0.024 0.003 TRP N 513 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.01370 (28630) covalent geometry : angle 0.81461 (40080) hydrogen bonds : bond 0.06741 ( 1116) hydrogen bonds : angle 5.01271 ( 3073) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 108 time to evaluate : 0.900 Fit side-chains REVERT: K 105 LEU cc_start: 0.0823 (OUTLIER) cc_final: 0.0355 (tt) REVERT: K 132 GLN cc_start: 0.5333 (OUTLIER) cc_final: 0.4941 (mm-40) REVERT: K 135 MET cc_start: 0.4108 (tpp) cc_final: 0.2999 (mpp) REVERT: K 348 MET cc_start: 0.1504 (mtp) cc_final: 0.0309 (ttt) REVERT: K 499 GLU cc_start: 0.6261 (mp0) cc_final: 0.5462 (tt0) REVERT: L 240 ILE cc_start: 0.1707 (OUTLIER) cc_final: 0.1441 (mm) REVERT: L 432 GLN cc_start: 0.2688 (OUTLIER) cc_final: 0.1038 (pp30) REVERT: L 461 MET cc_start: 0.3106 (OUTLIER) cc_final: 0.2619 (mmm) REVERT: G 17 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8602 (mtp180) REVERT: B 84 MET cc_start: 0.9069 (mmm) cc_final: 0.8842 (mmm) REVERT: C 95 LYS cc_start: 0.9540 (tptm) cc_final: 0.9062 (ttmt) REVERT: M 91 GLU cc_start: 0.3026 (mp0) cc_final: 0.2562 (tm-30) REVERT: M 517 ARG cc_start: 0.2740 (OUTLIER) cc_final: 0.2349 (ptm160) REVERT: N 516 LEU cc_start: -0.1061 (OUTLIER) cc_final: -0.1556 (mt) REVERT: A 129 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7757 (tmm160) outliers start: 96 outliers final: 29 residues processed: 193 average time/residue: 0.5964 time to fit residues: 135.6222 Evaluate side-chains 143 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 321 ILE Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 240 ILE Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain G residue 17 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain M residue 203 MET Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 459 VAL Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain N residue 523 THR Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 86 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 114 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 293 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 284 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 301 optimal weight: 0.5980 chunk 243 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 502 GLN L 80 HIS L 246 HIS ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 433 GLN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.157101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.096649 restraints weight = 73055.894| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 5.86 r_work: 0.3147 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28630 Z= 0.154 Angle : 0.590 12.500 40080 Z= 0.318 Chirality : 0.039 0.205 4633 Planarity : 0.004 0.058 4107 Dihedral : 26.377 161.179 6278 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.58 % Favored : 94.31 % Rotamer: Outliers : 2.75 % Allowed : 29.68 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2761 helix: 1.19 (0.15), residues: 1186 sheet: -1.50 (0.30), residues: 297 loop : -1.68 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 20 TYR 0.015 0.001 TYR H 39 PHE 0.012 0.001 PHE E 67 TRP 0.028 0.002 TRP N 513 HIS 0.007 0.001 HIS L 511 Details of bonding type rmsd covalent geometry : bond 0.00342 (28630) covalent geometry : angle 0.59001 (40080) hydrogen bonds : bond 0.03932 ( 1116) hydrogen bonds : angle 4.49719 ( 3073) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 118 time to evaluate : 0.900 Fit side-chains REVERT: K 132 GLN cc_start: 0.5509 (OUTLIER) cc_final: 0.4992 (mm-40) REVERT: K 135 MET cc_start: 0.3987 (tpp) cc_final: 0.2884 (mpp) REVERT: K 348 MET cc_start: 0.1276 (mtp) cc_final: 0.0232 (ttt) REVERT: K 499 GLU cc_start: 0.6259 (mp0) cc_final: 0.5476 (tt0) REVERT: L 432 GLN cc_start: 0.3251 (OUTLIER) cc_final: 0.1750 (pp30) REVERT: L 461 MET cc_start: 0.3080 (OUTLIER) cc_final: 0.2455 (mmm) REVERT: C 95 LYS cc_start: 0.9545 (tptm) cc_final: 0.9078 (ttmt) REVERT: M 91 GLU cc_start: 0.2973 (mp0) cc_final: 0.2569 (tm-30) REVERT: M 133 ASP cc_start: 0.1773 (t0) cc_final: 0.1551 (p0) REVERT: M 517 ARG cc_start: 0.2832 (OUTLIER) cc_final: 0.2285 (ptm160) REVERT: M 518 LEU cc_start: 0.1557 (OUTLIER) cc_final: 0.1282 (mp) REVERT: N 516 LEU cc_start: -0.1216 (OUTLIER) cc_final: -0.1620 (mt) REVERT: A 129 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7997 (tmm160) outliers start: 61 outliers final: 21 residues processed: 167 average time/residue: 0.6532 time to fit residues: 127.8583 Evaluate side-chains 140 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 203 MET Chi-restraints excluded: chain M residue 221 ILE Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 28 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 84 optimal weight: 50.0000 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 HIS L 246 HIS ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.155263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.092371 restraints weight = 72704.477| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 5.20 r_work: 0.3121 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 28630 Z= 0.315 Angle : 0.650 11.342 40080 Z= 0.350 Chirality : 0.044 0.194 4633 Planarity : 0.005 0.059 4107 Dihedral : 26.349 158.682 6278 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.30 % Rotamer: Outliers : 2.75 % Allowed : 30.27 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2761 helix: 1.13 (0.15), residues: 1184 sheet: -1.51 (0.30), residues: 295 loop : -1.72 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 252 TYR 0.022 0.001 TYR H 39 PHE 0.011 0.001 PHE H 67 TRP 0.030 0.002 TRP N 513 HIS 0.009 0.001 HIS L 246 Details of bonding type rmsd covalent geometry : bond 0.00733 (28630) covalent geometry : angle 0.64969 (40080) hydrogen bonds : bond 0.04753 ( 1116) hydrogen bonds : angle 4.57138 ( 3073) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 108 time to evaluate : 0.853 Fit side-chains REVERT: K 132 GLN cc_start: 0.5550 (OUTLIER) cc_final: 0.5064 (mm-40) REVERT: K 135 MET cc_start: 0.3835 (tpp) cc_final: 0.2978 (mpp) REVERT: K 348 MET cc_start: 0.1202 (mtp) cc_final: 0.0081 (ttt) REVERT: K 499 GLU cc_start: 0.6332 (mp0) cc_final: 0.5555 (tt0) REVERT: L 432 GLN cc_start: 0.3135 (OUTLIER) cc_final: 0.1570 (pp30) REVERT: L 461 MET cc_start: 0.3065 (OUTLIER) cc_final: 0.2407 (mmm) REVERT: B 84 MET cc_start: 0.8930 (mmm) cc_final: 0.8583 (mmm) REVERT: C 13 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.5276 (tttt) REVERT: C 95 LYS cc_start: 0.9523 (tptm) cc_final: 0.9047 (ttmt) REVERT: M 91 GLU cc_start: 0.2929 (mp0) cc_final: 0.2533 (tm-30) REVERT: M 133 ASP cc_start: 0.1793 (t0) cc_final: 0.1578 (p0) REVERT: M 517 ARG cc_start: 0.2857 (OUTLIER) cc_final: 0.2299 (ptm160) REVERT: M 518 LEU cc_start: 0.1523 (OUTLIER) cc_final: 0.1241 (mp) REVERT: N 516 LEU cc_start: -0.1136 (OUTLIER) cc_final: -0.1558 (mt) REVERT: A 129 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7887 (tmm160) outliers start: 61 outliers final: 26 residues processed: 158 average time/residue: 0.6499 time to fit residues: 121.3995 Evaluate side-chains 139 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 221 ILE Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 23 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain N residue 528 ILE Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 89 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 206 optimal weight: 0.4980 chunk 10 optimal weight: 30.0000 chunk 91 optimal weight: 0.0040 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 HIS ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN E 108 ASN D 81 ASN ** M 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.157397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098033 restraints weight = 73839.005| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 6.14 r_work: 0.3177 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28630 Z= 0.139 Angle : 0.573 10.819 40080 Z= 0.308 Chirality : 0.038 0.198 4633 Planarity : 0.004 0.055 4107 Dihedral : 25.925 160.199 6278 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 2.39 % Allowed : 30.85 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.16), residues: 2761 helix: 1.41 (0.15), residues: 1186 sheet: -1.39 (0.31), residues: 290 loop : -1.66 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.012 0.001 TYR H 39 PHE 0.017 0.001 PHE K 382 TRP 0.036 0.002 TRP N 513 HIS 0.035 0.001 HIS L 246 Details of bonding type rmsd covalent geometry : bond 0.00307 (28630) covalent geometry : angle 0.57267 (40080) hydrogen bonds : bond 0.03608 ( 1116) hydrogen bonds : angle 4.29024 ( 3073) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: K 132 GLN cc_start: 0.5512 (OUTLIER) cc_final: 0.5195 (mm-40) REVERT: K 135 MET cc_start: 0.3791 (tpp) cc_final: 0.2835 (mpp) REVERT: K 348 MET cc_start: 0.1258 (mtp) cc_final: 0.0174 (ttt) REVERT: K 499 GLU cc_start: 0.6313 (mp0) cc_final: 0.5551 (tt0) REVERT: L 432 GLN cc_start: 0.3268 (OUTLIER) cc_final: 0.1739 (pp30) REVERT: L 461 MET cc_start: 0.3150 (OUTLIER) cc_final: 0.2399 (mmm) REVERT: G 92 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: E 129 ARG cc_start: 0.8887 (tmt170) cc_final: 0.8662 (tmt170) REVERT: B 84 MET cc_start: 0.8821 (mmm) cc_final: 0.8568 (mmm) REVERT: B 95 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7641 (ptm160) REVERT: C 95 LYS cc_start: 0.9551 (tptm) cc_final: 0.9100 (ttmt) REVERT: M 91 GLU cc_start: 0.2847 (mp0) cc_final: 0.2454 (tm-30) REVERT: M 133 ASP cc_start: 0.1809 (t0) cc_final: 0.1605 (p0) REVERT: M 517 ARG cc_start: 0.2789 (OUTLIER) cc_final: 0.2273 (ptm160) REVERT: M 518 LEU cc_start: 0.1536 (OUTLIER) cc_final: 0.1288 (mp) REVERT: N 516 LEU cc_start: -0.1051 (OUTLIER) cc_final: -0.1467 (mt) REVERT: A 129 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8077 (tmm160) outliers start: 53 outliers final: 19 residues processed: 160 average time/residue: 0.6428 time to fit residues: 120.1776 Evaluate side-chains 138 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 511 VAL Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 221 ILE Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 482 ILE Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 164 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 225 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 267 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 255 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 HIS L 246 HIS ** L 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 ASN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.156086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.095319 restraints weight = 73075.486| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 4.96 r_work: 0.3126 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 28630 Z= 0.224 Angle : 0.603 11.026 40080 Z= 0.324 Chirality : 0.040 0.198 4633 Planarity : 0.004 0.058 4107 Dihedral : 25.962 157.873 6275 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 2.30 % Allowed : 30.90 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2761 helix: 1.36 (0.16), residues: 1185 sheet: -1.34 (0.31), residues: 295 loop : -1.64 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 35 TYR 0.018 0.001 TYR H 39 PHE 0.019 0.001 PHE K 382 TRP 0.042 0.002 TRP N 513 HIS 0.008 0.001 HIS L 511 Details of bonding type rmsd covalent geometry : bond 0.00518 (28630) covalent geometry : angle 0.60349 (40080) hydrogen bonds : bond 0.04162 ( 1116) hydrogen bonds : angle 4.36373 ( 3073) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 108 time to evaluate : 0.984 Fit side-chains REVERT: K 132 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.5019 (mm-40) REVERT: K 135 MET cc_start: 0.3707 (tpp) cc_final: 0.2633 (mpp) REVERT: K 346 MET cc_start: 0.5717 (ppp) cc_final: 0.5426 (ppp) REVERT: K 348 MET cc_start: 0.1284 (mtp) cc_final: 0.0040 (ttt) REVERT: K 499 GLU cc_start: 0.6310 (mp0) cc_final: 0.5554 (tt0) REVERT: L 242 ARG cc_start: 0.5388 (OUTLIER) cc_final: 0.4101 (mmp80) REVERT: L 247 TRP cc_start: 0.7120 (t60) cc_final: 0.6676 (t60) REVERT: L 432 GLN cc_start: 0.2783 (OUTLIER) cc_final: 0.1269 (pp30) REVERT: L 461 MET cc_start: 0.3123 (OUTLIER) cc_final: 0.2386 (mmm) REVERT: E 129 ARG cc_start: 0.8939 (tmt170) cc_final: 0.8699 (tmt170) REVERT: B 84 MET cc_start: 0.8922 (mmm) cc_final: 0.8634 (mmm) REVERT: C 95 LYS cc_start: 0.9521 (tptm) cc_final: 0.9064 (ttmt) REVERT: M 91 GLU cc_start: 0.2783 (mp0) cc_final: 0.2338 (tm-30) REVERT: M 133 ASP cc_start: 0.1789 (t0) cc_final: 0.1569 (p0) REVERT: M 517 ARG cc_start: 0.2746 (OUTLIER) cc_final: 0.2304 (ptm160) REVERT: N 245 ILE cc_start: 0.4283 (OUTLIER) cc_final: 0.4063 (mp) REVERT: N 364 VAL cc_start: 0.1872 (OUTLIER) cc_final: 0.1658 (t) REVERT: N 516 LEU cc_start: -0.1025 (OUTLIER) cc_final: -0.1485 (mt) REVERT: A 129 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7971 (tmm160) outliers start: 51 outliers final: 25 residues processed: 149 average time/residue: 0.6275 time to fit residues: 110.0683 Evaluate side-chains 142 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 511 VAL Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 242 ARG Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 221 ILE Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 482 ILE Chi-restraints excluded: chain N residue 508 ILE Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 54 optimal weight: 40.0000 chunk 233 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 40.0000 chunk 269 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 198 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 201 optimal weight: 20.0000 chunk 258 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 80 HIS L 246 HIS ** L 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 ASN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.157326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.097278 restraints weight = 73420.444| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 6.06 r_work: 0.3183 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28630 Z= 0.142 Angle : 0.575 10.529 40080 Z= 0.308 Chirality : 0.038 0.215 4633 Planarity : 0.004 0.056 4107 Dihedral : 25.791 158.979 6275 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 1.85 % Allowed : 31.39 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2761 helix: 1.47 (0.16), residues: 1186 sheet: -1.25 (0.31), residues: 290 loop : -1.63 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 35 TYR 0.013 0.001 TYR H 39 PHE 0.016 0.001 PHE K 382 TRP 0.047 0.002 TRP N 513 HIS 0.013 0.001 HIS L 246 Details of bonding type rmsd covalent geometry : bond 0.00320 (28630) covalent geometry : angle 0.57481 (40080) hydrogen bonds : bond 0.03559 ( 1116) hydrogen bonds : angle 4.24511 ( 3073) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 0.982 Fit side-chains REVERT: K 132 GLN cc_start: 0.5494 (OUTLIER) cc_final: 0.5168 (mm-40) REVERT: K 135 MET cc_start: 0.3840 (tpp) cc_final: 0.2893 (mpp) REVERT: K 346 MET cc_start: 0.5539 (ppp) cc_final: 0.5284 (ppp) REVERT: K 348 MET cc_start: 0.0880 (mtp) cc_final: -0.0167 (ttt) REVERT: K 499 GLU cc_start: 0.6326 (mp0) cc_final: 0.5567 (tt0) REVERT: L 432 GLN cc_start: 0.2850 (OUTLIER) cc_final: 0.1410 (pp30) REVERT: L 461 MET cc_start: 0.2976 (OUTLIER) cc_final: 0.2284 (mmm) REVERT: G 92 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8750 (mt-10) REVERT: E 129 ARG cc_start: 0.8908 (tmt170) cc_final: 0.8589 (tmt170) REVERT: B 95 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7710 (ptm160) REVERT: C 95 LYS cc_start: 0.9531 (tptm) cc_final: 0.9072 (ttmt) REVERT: M 91 GLU cc_start: 0.2903 (mp0) cc_final: 0.2493 (tm-30) REVERT: M 133 ASP cc_start: 0.1789 (t0) cc_final: 0.1579 (p0) REVERT: M 517 ARG cc_start: 0.2664 (OUTLIER) cc_final: 0.2206 (ptm160) REVERT: M 518 LEU cc_start: 0.1465 (OUTLIER) cc_final: 0.1236 (mp) REVERT: N 245 ILE cc_start: 0.4420 (OUTLIER) cc_final: 0.4193 (mp) REVERT: N 364 VAL cc_start: 0.1658 (OUTLIER) cc_final: 0.1455 (t) REVERT: N 516 LEU cc_start: -0.1077 (OUTLIER) cc_final: -0.1493 (mt) REVERT: A 129 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8020 (tmm160) outliers start: 41 outliers final: 24 residues processed: 144 average time/residue: 0.6554 time to fit residues: 110.5557 Evaluate side-chains 144 residues out of total 2475 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 132 GLN Chi-restraints excluded: chain K residue 204 HIS Chi-restraints excluded: chain K residue 452 ILE Chi-restraints excluded: chain K residue 511 VAL Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 243 HIS Chi-restraints excluded: chain L residue 246 HIS Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 351 VAL Chi-restraints excluded: chain L residue 432 GLN Chi-restraints excluded: chain L residue 461 MET Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain D residue 27 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 198 ILE Chi-restraints excluded: chain M residue 221 ILE Chi-restraints excluded: chain M residue 316 THR Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 517 ARG Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 245 ILE Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 482 ILE Chi-restraints excluded: chain N residue 508 ILE Chi-restraints excluded: chain N residue 516 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 200 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 239 optimal weight: 40.0000 chunk 256 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 86 optimal weight: 30.0000 chunk 1 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 416 GLN K 433 GLN L 80 HIS ** L 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 496 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** M 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 ASN ** M 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.153771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.091014 restraints weight = 72676.152| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 5.18 r_work: 0.3044 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.120 28630 Z= 0.478 Angle : 0.752 11.169 40080 Z= 0.402 Chirality : 0.051 0.308 4633 Planarity : 0.005 0.068 4107 Dihedral : 26.410 157.886 6275 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 2.30 % Allowed : 30.81 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2761 helix: 0.97 (0.15), residues: 1184 sheet: -1.34 (0.31), residues: 297 loop : -1.79 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 35 TYR 0.028 0.002 TYR H 39 PHE 0.019 0.002 PHE K 382 TRP 0.052 0.003 TRP N 513 HIS 0.018 0.002 HIS L 246 Details of bonding type rmsd covalent geometry : bond 0.01105 (28630) covalent geometry : angle 0.75204 (40080) hydrogen bonds : bond 0.05902 ( 1116) hydrogen bonds : angle 4.68349 ( 3073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23328.97 seconds wall clock time: 394 minutes 0.49 seconds (23640.49 seconds total)