Starting phenix.real_space_refine on Fri Feb 6 09:23:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvz_27022/02_2026/8cvz_27022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvz_27022/02_2026/8cvz_27022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cvz_27022/02_2026/8cvz_27022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvz_27022/02_2026/8cvz_27022.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvz_27022/02_2026/8cvz_27022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvz_27022/02_2026/8cvz_27022.cif" } resolution = 3.52 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= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 119 5.16 5 C 15760 2.51 5 N 4173 2.21 5 O 4465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.03s 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: 24517 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2057 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 247} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 4808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4808 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 24, 'TRANS': 577} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4781 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 24, 'TRANS': 575} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 4777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4777 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 24, 'TRANS': 576} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'HIS:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 4834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4834 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 576} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 295 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "I" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2100 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 253} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 295 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 285 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Time building chain proxies: 5.94, per 1000 atoms: 0.24 Number of scatterers: 24517 At special positions: 0 Unit cell: (125.245, 134.387, 160.899, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 119 16.00 O 4465 8.00 N 4173 7.00 C 15760 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: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5768 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 21 sheets defined 54.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'J' and resid 13 through 29 removed outlier: 3.754A pdb=" N GLY J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 53 removed outlier: 3.664A pdb=" N THR J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 88 through 92 Processing helix chain 'J' and resid 111 through 117 Processing helix chain 'J' and resid 142 through 156 Processing helix chain 'J' and resid 162 through 171 removed outlier: 3.503A pdb=" N ILE J 166 " --> pdb=" O GLY J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 176 Processing helix chain 'J' and resid 184 through 188 Processing helix chain 'J' and resid 191 through 197 Processing helix chain 'J' and resid 197 through 205 removed outlier: 3.653A pdb=" N PHE J 201 " --> pdb=" O TYR J 197 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 203 " --> pdb=" O PRO J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 257 removed outlier: 3.595A pdb=" N ILE J 252 " --> pdb=" O LEU J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 Processing helix chain 'B' and resid 42 through 59 removed outlier: 4.826A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 76 Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.526A pdb=" N LYS B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 145 through 169 Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.977A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 217 removed outlier: 3.814A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 376 through 411 Processing helix chain 'B' and resid 415 through 420 removed outlier: 4.310A pdb=" N LEU B 420 " --> pdb=" O MET B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.859A pdb=" N GLN B 436 " --> pdb=" O ILE B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 513 through 523 Processing helix chain 'B' and resid 532 through 542 Processing helix chain 'B' and resid 559 through 576 Processing helix chain 'B' and resid 578 through 590 Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.899A pdb=" N LEU B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 616 removed outlier: 4.281A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 616 " --> pdb=" O ALA B 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 4.359A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'C' and resid 84 through 97 Processing helix chain 'C' and resid 121 through 138 removed outlier: 3.984A pdb=" N ALA C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 168 Processing helix chain 'C' and resid 181 through 194 removed outlier: 4.139A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 217 removed outlier: 4.089A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 295 through 313 Processing helix chain 'C' and resid 338 through 356 removed outlier: 3.666A pdb=" N PHE C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 411 Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.693A pdb=" N GLY C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 513 through 522 Processing helix chain 'C' and resid 532 through 542 Processing helix chain 'C' and resid 559 through 576 Processing helix chain 'C' and resid 578 through 590 Processing helix chain 'C' and resid 591 through 592 No H-bonds generated for 'chain 'C' and resid 591 through 592' Processing helix chain 'C' and resid 593 through 596 Processing helix chain 'C' and resid 597 through 617 Processing helix chain 'D' and resid 42 through 59 removed outlier: 4.885A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 77 removed outlier: 3.526A pdb=" N VAL D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 97 removed outlier: 3.779A pdb=" N LYS D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.403A pdb=" N TRP D 124 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 138 Processing helix chain 'D' and resid 145 through 169 Processing helix chain 'D' and resid 181 through 183 No H-bonds generated for 'chain 'D' and resid 181 through 183' Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.985A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 217 removed outlier: 3.652A pdb=" N ARG D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 294 through 313 Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.586A pdb=" N PHE D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 411 Processing helix chain 'D' and resid 415 through 420 removed outlier: 4.138A pdb=" N LEU D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.516A pdb=" N MET D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 429 " --> pdb=" O PHE D 425 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 492 through 498 Processing helix chain 'D' and resid 513 through 522 Processing helix chain 'D' and resid 532 through 542 Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 559 through 576 Processing helix chain 'D' and resid 578 through 592 Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.892A pdb=" N LEU D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 616 removed outlier: 4.531A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 4.824A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.521A pdb=" N LYS A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 Processing helix chain 'A' and resid 146 through 169 Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.978A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.761A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.835A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 376 through 411 Processing helix chain 'A' and resid 415 through 420 removed outlier: 4.342A pdb=" N LEU A 420 " --> pdb=" O MET A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 513 through 523 Processing helix chain 'A' and resid 532 through 542 Processing helix chain 'A' and resid 559 through 576 Processing helix chain 'A' and resid 578 through 590 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.905A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 616 removed outlier: 4.300A pdb=" N ARG A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A 604 " --> pdb=" O TYR A 600 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 327 removed outlier: 3.604A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'I' and resid 13 through 29 removed outlier: 3.751A pdb=" N GLY I 18 " --> pdb=" O ALA I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 55 removed outlier: 3.626A pdb=" N VAL I 50 " --> pdb=" O SER I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 Processing helix chain 'I' and resid 80 through 88 removed outlier: 3.558A pdb=" N HIS I 88 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 142 through 156 Processing helix chain 'I' and resid 162 through 171 Processing helix chain 'I' and resid 172 through 176 Processing helix chain 'I' and resid 184 through 188 Processing helix chain 'I' and resid 191 through 197 Processing helix chain 'I' and resid 197 through 205 removed outlier: 3.723A pdb=" N PHE I 201 " --> pdb=" O TYR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 222 Processing helix chain 'I' and resid 238 through 242 removed outlier: 3.534A pdb=" N HIS I 242 " --> pdb=" O ASN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 257 removed outlier: 3.588A pdb=" N ILE I 252 " --> pdb=" O LEU I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 264 Processing helix chain 'F' and resid 318 through 327 removed outlier: 3.725A pdb=" N LYS F 322 " --> pdb=" O SER F 318 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'G' and resid 318 through 327 removed outlier: 3.723A pdb=" N LYS G 322 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU G 323 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'H' and resid 318 through 327 removed outlier: 3.724A pdb=" N LYS H 322 " --> pdb=" O SER H 318 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU H 323 " --> pdb=" O GLU H 319 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 348 removed outlier: 4.113A pdb=" N TYR H 348 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 57 through 60 removed outlier: 7.041A pdb=" N GLN J 4 " --> pdb=" O ARG J 34 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL J 36 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE J 6 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU J 38 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N THR J 8 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU J 9 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL J 136 " --> pdb=" O ALA J 123 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA J 123 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 105 through 107 removed outlier: 3.705A pdb=" N HIS J 212 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79 removed outlier: 6.300A pdb=" N TYR B 62 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL B 115 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU B 29 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 65 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 31 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 200 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR B 256 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE B 202 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE B 255 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.543A pdb=" N VAL B 362 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 476 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA B 364 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N THR B 529 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU B 553 " --> pdb=" O SER B 526 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER B 528 " --> pdb=" O LEU B 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 374 through 375 removed outlier: 3.936A pdb=" N ASN B 374 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.654A pdb=" N VAL C 28 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS C 178 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL C 175 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE C 201 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA C 177 " --> pdb=" O ILE C 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 67 removed outlier: 6.580A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.713A pdb=" N THR C 257 " --> pdb=" O ILE C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 475 removed outlier: 6.535A pdb=" N VAL C 362 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 372 through 375 removed outlier: 4.146A pdb=" N ASN C 374 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 62 through 63 removed outlier: 8.525A pdb=" N PHE D 63 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU D 29 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL D 175 " --> pdb=" O ALA D 199 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 201 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 257 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'D' and resid 473 through 478 removed outlier: 6.546A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE D 476 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA D 364 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS D 478 " --> pdb=" O ALA D 364 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE D 366 " --> pdb=" O HIS D 478 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE D 367 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR D 529 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N PHE D 505 " --> pdb=" O THR D 529 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU D 553 " --> pdb=" O SER D 526 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER D 528 " --> pdb=" O LEU D 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 372 through 375 removed outlier: 7.032A pdb=" N ASN D 447 " --> pdb=" O ASN D 373 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.302A pdb=" N TYR A 62 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL A 115 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 29 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 65 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 200 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR A 256 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 202 " --> pdb=" O THR A 256 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE A 255 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.547A pdb=" N VAL A 362 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE A 476 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA A 364 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE A 367 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 328 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N THR A 529 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 553 " --> pdb=" O SER A 526 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 528 " --> pdb=" O LEU A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.565A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.636A pdb=" N ILE I 59 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS I 97 " --> pdb=" O ASP I 3 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU I 9 " --> pdb=" O MET I 101 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL I 136 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA I 123 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER I 121 " --> pdb=" O VAL I 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 105 through 107 removed outlier: 6.287A pdb=" N LEU I 189 " --> pdb=" O HIS I 212 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 224 through 225 1169 hydrogen bonds defined for protein. 3402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4241 1.32 - 1.45: 7485 1.45 - 1.58: 13252 1.58 - 1.71: 0 1.71 - 1.85: 180 Bond restraints: 25158 Sorted by residual: bond pdb=" CE1 HIS C 311 " pdb=" NE2 HIS C 311 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.71e+01 bond pdb=" CA ALA B 37 " pdb=" CB ALA B 37 " ideal model delta sigma weight residual 1.537 1.484 0.053 1.38e-02 5.25e+03 1.49e+01 bond pdb=" C VAL C 32 " pdb=" O VAL C 32 " ideal model delta sigma weight residual 1.238 1.197 0.040 1.06e-02 8.90e+03 1.43e+01 bond pdb=" CA SER D 169 " pdb=" CB SER D 169 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.26e-02 6.30e+03 1.37e+01 bond pdb=" CA SER C 528 " pdb=" CB SER C 528 " ideal model delta sigma weight residual 1.527 1.473 0.054 1.49e-02 4.50e+03 1.33e+01 ... (remaining 25153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 32138 3.02 - 6.03: 1895 6.03 - 9.05: 111 9.05 - 12.07: 4 12.07 - 15.08: 3 Bond angle restraints: 34151 Sorted by residual: angle pdb=" C PRO D 112 " pdb=" CA PRO D 112 " pdb=" CB PRO D 112 " ideal model delta sigma weight residual 111.46 100.37 11.09 1.21e+00 6.83e-01 8.41e+01 angle pdb=" C THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta sigma weight residual 109.24 124.32 -15.08 1.75e+00 3.27e-01 7.43e+01 angle pdb=" C THR B 49 " pdb=" CA THR B 49 " pdb=" CB THR B 49 " ideal model delta sigma weight residual 109.24 123.83 -14.59 1.75e+00 3.27e-01 6.95e+01 angle pdb=" C THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta sigma weight residual 109.24 123.61 -14.37 1.75e+00 3.27e-01 6.74e+01 angle pdb=" C PRO C 506 " pdb=" CA PRO C 506 " pdb=" CB PRO C 506 " ideal model delta sigma weight residual 111.11 101.99 9.12 1.17e+00 7.31e-01 6.08e+01 ... (remaining 34146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13178 17.89 - 35.78: 1183 35.78 - 53.67: 323 53.67 - 71.56: 52 71.56 - 89.45: 6 Dihedral angle restraints: 14742 sinusoidal: 5796 harmonic: 8946 Sorted by residual: dihedral pdb=" C THR A 49 " pdb=" N THR A 49 " pdb=" CA THR A 49 " pdb=" CB THR A 49 " ideal model delta harmonic sigma weight residual -122.00 -143.81 21.81 0 2.50e+00 1.60e-01 7.61e+01 dihedral pdb=" C THR B 49 " pdb=" N THR B 49 " pdb=" CA THR B 49 " pdb=" CB THR B 49 " ideal model delta harmonic sigma weight residual -122.00 -143.32 21.32 0 2.50e+00 1.60e-01 7.27e+01 dihedral pdb=" C THR D 49 " pdb=" N THR D 49 " pdb=" CA THR D 49 " pdb=" CB THR D 49 " ideal model delta harmonic sigma weight residual -122.00 -143.28 21.28 0 2.50e+00 1.60e-01 7.25e+01 ... (remaining 14739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2992 0.160 - 0.320: 649 0.320 - 0.480: 71 0.480 - 0.640: 5 0.640 - 0.799: 3 Chirality restraints: 3720 Sorted by residual: chirality pdb=" CA THR A 49 " pdb=" N THR A 49 " pdb=" C THR A 49 " pdb=" CB THR A 49 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" CA THR D 49 " pdb=" N THR D 49 " pdb=" C THR D 49 " pdb=" CB THR D 49 " both_signs ideal model delta sigma weight residual False 2.53 1.74 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA THR B 49 " pdb=" N THR B 49 " pdb=" C THR B 49 " pdb=" CB THR B 49 " both_signs ideal model delta sigma weight residual False 2.53 1.74 0.78 2.00e-01 2.50e+01 1.53e+01 ... (remaining 3717 not shown) Planarity restraints: 4381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 572 " -0.079 2.00e-02 2.50e+03 4.27e-02 3.64e+01 pdb=" CG TYR C 572 " 0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR C 572 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR C 572 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 572 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 572 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 572 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 572 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 62 " 0.027 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C TYR C 62 " -0.093 2.00e-02 2.50e+03 pdb=" O TYR C 62 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE C 63 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 154 " 0.023 2.00e-02 2.50e+03 3.84e-02 2.58e+01 pdb=" CG PHE B 154 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE B 154 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE B 154 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 154 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 154 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE B 154 " -0.022 2.00e-02 2.50e+03 ... (remaining 4378 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 366 2.67 - 3.23: 23177 3.23 - 3.79: 40442 3.79 - 4.34: 56360 4.34 - 4.90: 88834 Nonbonded interactions: 209179 Sorted by model distance: nonbonded pdb=" O THR C 204 " pdb=" OG1 THR C 204 " model vdw 2.118 3.040 nonbonded pdb=" N VAL B 32 " pdb=" O HIS B 178 " model vdw 2.316 3.120 nonbonded pdb=" OG1 THR D 361 " pdb=" NH2 ARG D 472 " model vdw 2.337 3.120 nonbonded pdb=" O PHE B 30 " pdb=" N HIS B 178 " model vdw 2.373 3.120 nonbonded pdb=" N PHE B 30 " pdb=" O VAL B 176 " model vdw 2.413 3.120 ... (remaining 209174 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 22 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 69 or (resid 70 and ( \ name N or name CA or name C or name O or name CB )) or resid 71 through 73 or (r \ esid 74 and (name N or name CA or name C or name O or name CB )) or resid 75 thr \ ough 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) \ or resid 110 through 126 or (resid 127 through 128 and (name N or name CA or nam \ e C or name O or name CB )) or resid 129 through 131 or (resid 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 143 or (resid 1 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 145 through \ 175 or (resid 176 through 177 and (name N or name CA or name C or name O or nam \ e CB )) or resid 178 through 180 or (resid 181 and (name N or name CA or name C \ or name O or name CB )) or resid 182 through 194 or (resid 195 and (name N or na \ me CA or name C or name O or name CB )) or resid 196 through 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 236 \ or (resid 237 and (name N or name CA or name C or name O or name CB )) or resid \ 238 through 252 or (resid 253 and (name N or name CA or name C or name O or nam \ e CB )) or resid 254 through 259 or (resid 260 and (name N or name CA or name C \ or name O or name CB )) or resid 261 through 284 or (resid 285 through 286 and ( \ name N or name CA or name C or name O or name CB )) or resid 287 or resid 293 or \ (resid 294 and (name N or name CA or name C or name O or name CB )) or resid 29 \ 5 through 302 or (resid 303 and (name N or name CA or name C or name O or name C \ B )) or resid 304 through 332 or (resid 333 and (name N or name CA or name C or \ name O or name CB )) or resid 334 through 339 or (resid 340 and (name N or name \ CA or name C or name O or name CB )) or resid 341 through 370 or (resid 371 and \ (name N or name CA or name C or name O or name CB )) or resid 372 through 405 or \ (resid 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 414 or (resid 415 through 418 and (name N or name CA or name C or name \ O or name CB )) or resid 419 through 420 or (resid 421 through 423 and (name N \ or name CA or name C or name O or name CB )) or resid 424 through 429 or (resid \ 430 through 431 and (name N or name CA or name C or name O or name CB )) or resi \ d 432 through 436 or (resid 437 and (name N or name CA or name C or name O or na \ me CB )) or resid 438 through 446 or (resid 447 through 448 and (name N or name \ CA or name C or name O or name CB )) or resid 449 through 480 or (resid 481 and \ (name N or name CA or name C or name O or name CB )) or resid 482 through 509 or \ (resid 510 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 1 through 590 or (resid 591 and (name N or name CA or name C or name O or name C \ B )) or resid 592 through 596 or (resid 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 605 or (resid 606 and (name N or name \ CA or name C or name O or name CB )) or resid 607 through 608 or (resid 609 and \ (name N or name CA or name C or name O or name CB )) or resid 610 through 621 or \ (resid 622 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 3 through 626)) selection = (chain 'B' and (resid 22 through 55 or (resid 56 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 59 or (resid 60 and (na \ me N or name CA or name C or name O or name CB )) or resid 61 through 69 or (res \ id 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throu \ gh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or r \ esid 75 through 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB )) or resid 110 through 126 or (resid 127 through 128 and (name N or nam \ e CA or name C or name O or name CB )) or resid 129 through 131 or (resid 132 an \ d (name N or name CA or name C or name O or name CB )) or resid 133 through 143 \ or (resid 144 and (name N or name CA or name C or name O or name CB )) or resid \ 145 through 180 or (resid 181 and (name N or name CA or name C or name O or name \ CB )) or resid 182 through 194 or (resid 195 and (name N or name CA or name C o \ r name O or name CB )) or resid 196 through 230 or (resid 231 and (name N or nam \ e CA or name C or name O or name CB )) or resid 232 through 236 or (resid 237 an \ d (name N or name CA or name C or name O or name CB )) or resid 238 through 252 \ or (resid 253 and (name N or name CA or name C or name O or name CB )) or resid \ 254 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 284 or (resid 285 through 286 and (name N or name CA \ or name C or name O or name CB )) or resid 287 or resid 293 or (resid 294 and ( \ name N or name CA or name C or name O or name CB )) or resid 295 through 339 or \ (resid 340 and (name N or name CA or name C or name O or name CB )) or resid 341 \ through 370 or (resid 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 405 or (resid 406 and (name N or name CA or name C or n \ ame O or name CB )) or resid 407 through 415 or (resid 416 through 418 and (name \ N or name CA or name C or name O or name CB )) or resid 419 through 420 or (res \ id 421 through 423 and (name N or name CA or name C or name O or name CB )) or r \ esid 424 through 447 or (resid 448 and (name N or name CA or name C or name O or \ name CB )) or resid 449 through 480 or (resid 481 and (name N or name CA or nam \ e C or name O or name CB )) or resid 482 through 590 or (resid 591 and (name N o \ r name CA or name C or name O or name CB )) or resid 592 through 596 or (resid 5 \ 97 and (name N or name CA or name C or name O or name CB )) or resid 598 through \ 626)) selection = (chain 'C' and (resid 22 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 55 or (resid 56 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 69 or (res \ id 70 and (name N or name CA or name C or name O or name CB )) or resid 71 throu \ gh 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or r \ esid 75 through 126 or (resid 127 through 128 and (name N or name CA or name C o \ r name O or name CB )) or resid 129 through 131 or (resid 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 175 or (resid 176 th \ rough 177 and (name N or name CA or name C or name O or name CB )) or resid 178 \ through 194 or (resid 195 and (name N or name CA or name C or name O or name CB \ )) or resid 196 through 259 or (resid 260 and (name N or name CA or name C or na \ me O or name CB )) or resid 261 through 284 or (resid 285 through 286 and (name \ N or name CA or name C or name O or name CB )) or resid 287 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB )) or resid 304 thro \ ugh 332 or (resid 333 and (name N or name CA or name C or name O or name CB )) o \ r resid 334 through 414 or (resid 415 through 418 and (name N or name CA or name \ C or name O or name CB )) or resid 419 through 429 or (resid 430 through 431 an \ d (name N or name CA or name C or name O or name CB )) or resid 432 through 436 \ or (resid 437 and (name N or name CA or name C or name O or name CB )) or resid \ 438 through 446 or (resid 447 through 448 and (name N or name CA or name C or na \ me O or name CB )) or resid 449 through 509 or (resid 510 and (name N or name CA \ or name C or name O or name CB )) or resid 511 through 590 or (resid 591 and (n \ ame N or name CA or name C or name O or name CB )) or resid 592 through 596 or ( \ resid 597 and (name N or name CA or name C or name O or name CB )) or resid 598 \ through 605 or (resid 606 and (name N or name CA or name C or name O or name CB \ )) or resid 607 through 608 or (resid 609 and (name N or name CA or name C or na \ me O or name CB )) or resid 610 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 621 or (resid 622 and (n \ ame N or name CA or name C or name O or name CB )) or resid 623 through 626)) selection = (chain 'D' and (resid 22 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 55 or (resid 56 through 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throu \ gh 143 or (resid 144 and (name N or name CA or name C or name O or name CB )) or \ resid 145 through 175 or (resid 176 through 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 180 or (resid 181 and (name N or \ name CA or name C or name O or name CB )) or resid 182 through 236 or (resid 237 \ and (name N or name CA or name C or name O or name CB )) or resid 238 through 2 \ 85 or (resid 286 and (name N or name CA or name C or name O or name CB )) or res \ id 287 through 302 or (resid 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 304 through 332 or (resid 333 and (name N or name CA or name \ C or name O or name CB )) or resid 334 through 339 or (resid 340 and (name N or \ name CA or name C or name O or name CB )) or resid 341 through 370 or (resid 371 \ and (name N or name CA or name C or name O or name CB )) or resid 372 through 4 \ 05 or (resid 406 and (name N or name CA or name C or name O or name CB )) or res \ id 407 through 414 or (resid 415 through 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 through 429 or (resid 430 through 431 and (na \ me N or name CA or name C or name O or name CB )) or resid 432 through 436 or (r \ esid 437 and (name N or name CA or name C or name O or name CB )) or resid 438 t \ hrough 446 or (resid 447 through 448 and (name N or name CA or name C or name O \ or name CB )) or resid 449 through 480 or (resid 481 and (name N or name CA or n \ ame C or name O or name CB )) or resid 482 through 509 or (resid 510 and (name N \ or name CA or name C or name O or name CB )) or resid 511 through 605 or (resid \ 606 and (name N or name CA or name C or name O or name CB )) or resid 607 throu \ gh 608 or (resid 609 and (name N or name CA or name C or name O or name CB )) or \ resid 610 through 618 or (resid 619 and (name N or name CA or name C or name O \ or name CB )) or resid 620 through 621 or (resid 622 and (name N or name CA or n \ ame C or name O or name CB )) or resid 623 through 626)) } ncs_group { reference = (chain 'E' and resid 316 through 349) selection = (chain 'F' and resid 316 through 349) selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 232 or resid 238 through 262 or (resid 263 and ( \ name N or name CA or name C or name O or name CB )) or resid 264 through 266)) selection = (chain 'J' and (resid 1 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB )) or resid 164 through 266)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 23.290 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.008 0.057 25158 Z= 0.555 Angle : 1.574 15.081 34151 Z= 1.076 Chirality : 0.131 0.799 3720 Planarity : 0.009 0.054 4381 Dihedral : 14.871 89.453 8974 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.99 % Favored : 96.94 % Rotamer: Outliers : 5.85 % Allowed : 10.69 % Favored : 83.46 % Cbeta Deviations : 1.39 % 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: -0.25 (0.14), residues: 3040 helix: 0.86 (0.12), residues: 1504 sheet: -1.30 (0.27), residues: 383 loop : -1.04 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG D 555 TYR 0.081 0.008 TYR C 572 PHE 0.073 0.009 PHE B 154 TRP 0.064 0.009 TRP C 34 HIS 0.026 0.007 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00819 (25158) covalent geometry : angle 1.57373 (34151) hydrogen bonds : bond 0.19587 ( 1169) hydrogen bonds : angle 7.25412 ( 3402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 732 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 60 MET cc_start: 0.7787 (mmm) cc_final: 0.7535 (mmm) REVERT: J 95 TYR cc_start: 0.7608 (m-80) cc_final: 0.7125 (m-80) REVERT: J 113 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7669 (t0) REVERT: J 130 ASP cc_start: 0.8313 (m-30) cc_final: 0.7227 (m-30) REVERT: B 24 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.6008 (mt) REVERT: B 108 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.5766 (pp) REVERT: B 116 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.4248 (tp) REVERT: B 171 GLU cc_start: 0.2827 (OUTLIER) cc_final: 0.2440 (tp30) REVERT: B 292 GLU cc_start: 0.1888 (OUTLIER) cc_final: -0.0224 (tt0) REVERT: B 296 LEU cc_start: 0.5286 (mp) cc_final: 0.5045 (mt) REVERT: B 319 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8236 (m-40) REVERT: B 337 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6868 (ttmm) REVERT: B 361 THR cc_start: 0.8518 (m) cc_final: 0.8227 (p) REVERT: B 463 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 542 ILE cc_start: 0.3393 (tp) cc_final: 0.3004 (pt) REVERT: C 62 TYR cc_start: 0.8288 (t80) cc_final: 0.7397 (t80) REVERT: C 80 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7623 (mp) REVERT: C 106 TRP cc_start: 0.8547 (t60) cc_final: 0.8276 (t60) REVERT: C 229 VAL cc_start: 0.7842 (p) cc_final: 0.7402 (p) REVERT: C 372 THR cc_start: 0.7593 (OUTLIER) cc_final: 0.7381 (t) REVERT: C 448 MET cc_start: 0.8235 (mmm) cc_final: 0.7857 (mmt) REVERT: C 562 ASP cc_start: 0.8282 (m-30) cc_final: 0.7942 (t0) REVERT: C 579 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7627 (ttt-90) REVERT: C 603 ARG cc_start: 0.6989 (ttp80) cc_final: 0.6619 (tmt170) REVERT: D 68 TYR cc_start: 0.7543 (t80) cc_final: 0.7331 (t80) REVERT: D 100 LYS cc_start: 0.8266 (mttt) cc_final: 0.7769 (tptt) REVERT: D 138 ASN cc_start: 0.7433 (OUTLIER) cc_final: 0.7201 (m110) REVERT: D 147 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7554 (mm-30) REVERT: D 259 SER cc_start: 0.8227 (t) cc_final: 0.7790 (p) REVERT: D 333 GLU cc_start: 0.7025 (tp30) cc_final: 0.6720 (tp30) REVERT: D 337 LYS cc_start: 0.8327 (mptp) cc_final: 0.8023 (tptt) REVERT: D 387 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8313 (tptt) REVERT: D 419 MET cc_start: 0.7604 (mmp) cc_final: 0.7336 (mmp) REVERT: D 480 GLU cc_start: 0.8261 (tt0) cc_final: 0.7962 (tp30) REVERT: D 491 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8259 (m) REVERT: D 579 ARG cc_start: 0.7641 (mmm-85) cc_final: 0.7427 (tpp80) REVERT: D 619 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7796 (pm20) REVERT: A 48 GLN cc_start: 0.8029 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 70 GLU cc_start: 0.8467 (tt0) cc_final: 0.8153 (mt-10) REVERT: A 109 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8009 (pm20) REVERT: A 135 ASP cc_start: 0.8431 (m-30) cc_final: 0.8044 (t70) REVERT: A 303 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8070 (tpt170) REVERT: A 319 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8368 (t0) REVERT: A 422 LYS cc_start: 0.7938 (pttt) cc_final: 0.7668 (tppt) REVERT: A 423 GLU cc_start: 0.8644 (pt0) cc_final: 0.8301 (tp30) REVERT: A 586 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6895 (tpp80) REVERT: A 600 TYR cc_start: 0.7686 (t80) cc_final: 0.7457 (t80) REVERT: E 316 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.5984 (t) REVERT: E 317 SER cc_start: 0.6859 (OUTLIER) cc_final: 0.6294 (p) REVERT: I 30 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.7530 (mmt180) REVERT: I 156 GLN cc_start: 0.8574 (mt0) cc_final: 0.8272 (tm-30) REVERT: H 316 VAL cc_start: 0.2848 (OUTLIER) cc_final: 0.2582 (t) REVERT: H 333 MET cc_start: 0.8392 (mmm) cc_final: 0.8080 (pmm) outliers start: 152 outliers final: 46 residues processed: 829 average time/residue: 0.1901 time to fit residues: 238.6464 Evaluate side-chains 508 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 446 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 113 ASP Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 198 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain G residue 317 SER Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 348 TYR Chi-restraints excluded: chain H residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.0060 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 GLN J 140 GLN J 164 GLN B 95 ASN B 138 ASN ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN B 417 ASN B 541 HIS B 581 GLN B 587 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 283 ASN C 295 ASN C 299 GLN C 388 GLN C 436 GLN C 467 ASN D 305 GLN D 360 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 GLN D 581 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS A 260 GLN A 299 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN A 388 GLN A 417 ASN A 446 HIS A 530 ASN A 577 GLN A 587 ASN E 350 GLN I 28 GLN I 140 GLN I 164 GLN I 236 HIS I 256 ASN F 350 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.198722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154254 restraints weight = 30923.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154093 restraints weight = 21994.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155351 restraints weight = 23829.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158160 restraints weight = 15091.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159355 restraints weight = 11979.113| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25158 Z= 0.166 Angle : 0.645 9.459 34151 Z= 0.344 Chirality : 0.045 0.216 3720 Planarity : 0.004 0.055 4381 Dihedral : 7.493 70.742 3449 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.69 % Allowed : 15.73 % Favored : 79.58 % 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: 0.53 (0.15), residues: 3040 helix: 1.54 (0.13), residues: 1531 sheet: -1.18 (0.26), residues: 384 loop : -0.67 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 105 TYR 0.031 0.002 TYR C 313 PHE 0.028 0.002 PHE C 156 TRP 0.026 0.002 TRP B 34 HIS 0.009 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00363 (25158) covalent geometry : angle 0.64453 (34151) hydrogen bonds : bond 0.05329 ( 1169) hydrogen bonds : angle 5.42107 ( 3402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 467 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7736 (m) cc_final: 0.7431 (t) REVERT: J 95 TYR cc_start: 0.7294 (m-80) cc_final: 0.6627 (m-80) REVERT: J 125 ASP cc_start: 0.8524 (t0) cc_final: 0.8195 (t0) REVERT: B 292 GLU cc_start: 0.1861 (OUTLIER) cc_final: 0.0779 (tt0) REVERT: B 319 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7928 (m-40) REVERT: B 424 ASP cc_start: 0.7337 (p0) cc_final: 0.7054 (p0) REVERT: B 548 TYR cc_start: 0.5225 (OUTLIER) cc_final: 0.4954 (t80) REVERT: B 600 TYR cc_start: 0.5834 (t80) cc_final: 0.5629 (t80) REVERT: C 24 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6192 (pp) REVERT: C 204 THR cc_start: 0.8983 (p) cc_final: 0.8762 (t) REVERT: C 212 TYR cc_start: 0.7658 (m-80) cc_final: 0.7379 (m-10) REVERT: C 331 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8048 (mtm110) REVERT: C 416 MET cc_start: 0.8021 (mmm) cc_final: 0.7767 (mmm) REVERT: C 530 ASN cc_start: 0.7766 (t0) cc_final: 0.7403 (t0) REVERT: C 606 MET cc_start: 0.6592 (mtm) cc_final: 0.6371 (mtm) REVERT: D 100 LYS cc_start: 0.7770 (mttt) cc_final: 0.7200 (tptt) REVERT: D 174 HIS cc_start: 0.6452 (m-70) cc_final: 0.6048 (m90) REVERT: D 333 GLU cc_start: 0.6400 (tp30) cc_final: 0.6156 (mm-30) REVERT: D 387 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8421 (tptt) REVERT: D 522 MET cc_start: 0.8565 (mtp) cc_final: 0.8306 (mtt) REVERT: D 611 MET cc_start: 0.6897 (mmm) cc_final: 0.6591 (mtt) REVERT: A 35 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: A 100 LYS cc_start: 0.6865 (mtmp) cc_final: 0.6094 (mtmm) REVERT: A 102 TYR cc_start: 0.7565 (m-80) cc_final: 0.7172 (m-10) REVERT: A 466 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: A 572 TYR cc_start: 0.7514 (t80) cc_final: 0.7260 (t80) REVERT: A 586 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6751 (tpp80) REVERT: E 333 MET cc_start: 0.8394 (mmm) cc_final: 0.7967 (mtt) REVERT: I 30 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7377 (mmt180) outliers start: 122 outliers final: 55 residues processed: 557 average time/residue: 0.1774 time to fit residues: 154.4545 Evaluate side-chains 452 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 390 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 301 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 185 optimal weight: 6.9990 chunk 281 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 4 GLN ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS C 222 ASN D 383 GLN A 95 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN E 329 GLN I 182 HIS I 239 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.196303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.151907 restraints weight = 30965.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152051 restraints weight = 22258.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153798 restraints weight = 21847.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.155648 restraints weight = 14461.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.156613 restraints weight = 12320.844| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25158 Z= 0.149 Angle : 0.591 12.721 34151 Z= 0.310 Chirality : 0.043 0.264 3720 Planarity : 0.004 0.072 4381 Dihedral : 6.294 70.288 3390 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.85 % Allowed : 17.69 % Favored : 78.46 % 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: 0.53 (0.15), residues: 3040 helix: 1.51 (0.13), residues: 1536 sheet: -1.30 (0.26), residues: 389 loop : -0.56 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 437 TYR 0.028 0.002 TYR H 332 PHE 0.036 0.002 PHE D 312 TRP 0.023 0.002 TRP B 34 HIS 0.010 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00337 (25158) covalent geometry : angle 0.59088 (34151) hydrogen bonds : bond 0.04553 ( 1169) hydrogen bonds : angle 5.10531 ( 3402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 420 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7673 (m) cc_final: 0.7219 (t) REVERT: J 95 TYR cc_start: 0.7366 (m-80) cc_final: 0.6740 (m-80) REVERT: J 125 ASP cc_start: 0.8455 (t70) cc_final: 0.7939 (t0) REVERT: J 130 ASP cc_start: 0.7991 (m-30) cc_final: 0.6653 (m-30) REVERT: J 163 ASP cc_start: 0.8010 (p0) cc_final: 0.7700 (p0) REVERT: B 319 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8105 (m-40) REVERT: B 542 ILE cc_start: 0.6059 (mm) cc_final: 0.4696 (pt) REVERT: B 548 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.5187 (t80) REVERT: B 600 TYR cc_start: 0.5855 (t80) cc_final: 0.5632 (t80) REVERT: C 24 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6225 (pp) REVERT: C 331 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8199 (mtm110) REVERT: C 528 SER cc_start: 0.8523 (t) cc_final: 0.8048 (m) REVERT: C 530 ASN cc_start: 0.7897 (t0) cc_final: 0.7495 (t0) REVERT: C 552 ILE cc_start: 0.9040 (mm) cc_final: 0.8810 (mm) REVERT: C 611 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6696 (mtt) REVERT: C 615 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7906 (ttmt) REVERT: D 100 LYS cc_start: 0.7747 (mttt) cc_final: 0.7134 (mmmt) REVERT: D 522 MET cc_start: 0.8516 (mtp) cc_final: 0.8313 (mtt) REVERT: D 539 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6129 (mt-10) REVERT: A 35 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: A 43 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8153 (mt) REVERT: A 100 LYS cc_start: 0.6890 (mtmp) cc_final: 0.6129 (mtmm) REVERT: A 102 TYR cc_start: 0.7482 (m-80) cc_final: 0.7101 (m-10) REVERT: A 526 SER cc_start: 0.8314 (p) cc_final: 0.8084 (m) REVERT: A 586 ARG cc_start: 0.6963 (mmm160) cc_final: 0.6688 (tpp80) REVERT: E 333 MET cc_start: 0.8482 (mmm) cc_final: 0.7983 (mtt) REVERT: I 30 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7388 (mmt-90) REVERT: H 321 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8147 (mtp-110) outliers start: 100 outliers final: 58 residues processed: 491 average time/residue: 0.1692 time to fit residues: 132.1677 Evaluate side-chains 433 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 367 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 300 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 267 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS B 205 HIS B 222 ASN B 226 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 501 HIS B 585 GLN C 180 HIS ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS A 576 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.189258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.146191 restraints weight = 31174.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144514 restraints weight = 25520.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146141 restraints weight = 28098.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148412 restraints weight = 17355.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149332 restraints weight = 13986.305| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 25158 Z= 0.300 Angle : 0.705 13.634 34151 Z= 0.369 Chirality : 0.047 0.234 3720 Planarity : 0.005 0.063 4381 Dihedral : 6.095 57.512 3375 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.23 % Allowed : 17.38 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3040 helix: 1.06 (0.13), residues: 1533 sheet: -1.70 (0.26), residues: 390 loop : -0.70 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 48 TYR 0.026 0.003 TYR A 313 PHE 0.030 0.003 PHE D 312 TRP 0.027 0.002 TRP B 106 HIS 0.009 0.002 HIS D 446 Details of bonding type rmsd covalent geometry : bond 0.00704 (25158) covalent geometry : angle 0.70516 (34151) hydrogen bonds : bond 0.04715 ( 1169) hydrogen bonds : angle 5.25437 ( 3402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 388 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7778 (m) cc_final: 0.7511 (t) REVERT: J 95 TYR cc_start: 0.7422 (m-80) cc_final: 0.6705 (m-80) REVERT: J 125 ASP cc_start: 0.8628 (t70) cc_final: 0.8240 (t0) REVERT: B 351 TYR cc_start: 0.6767 (t80) cc_final: 0.6471 (m-80) REVERT: B 541 HIS cc_start: 0.5995 (OUTLIER) cc_final: 0.5793 (m-70) REVERT: B 588 ARG cc_start: 0.6482 (mmt-90) cc_final: 0.6199 (mmt-90) REVERT: C 30 PHE cc_start: 0.8306 (m-10) cc_final: 0.8072 (m-80) REVERT: C 243 CYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6580 (m) REVERT: C 277 VAL cc_start: 0.8895 (t) cc_final: 0.8592 (m) REVERT: C 331 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8290 (mtm110) REVERT: C 595 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8174 (tt) REVERT: C 615 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7856 (ttmt) REVERT: D 68 TYR cc_start: 0.7041 (t80) cc_final: 0.6769 (t80) REVERT: D 100 LYS cc_start: 0.7674 (mttt) cc_final: 0.7262 (tptt) REVERT: D 147 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7820 (mm-30) REVERT: D 180 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8320 (m170) REVERT: D 336 ASN cc_start: 0.8202 (m-40) cc_final: 0.7852 (m-40) REVERT: D 522 MET cc_start: 0.8534 (mtp) cc_final: 0.8275 (mtt) REVERT: A 100 LYS cc_start: 0.7165 (mtmp) cc_final: 0.6492 (mtmm) REVERT: A 102 TYR cc_start: 0.7625 (m-80) cc_final: 0.7207 (m-10) REVERT: A 466 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: A 509 TYR cc_start: 0.8050 (t80) cc_final: 0.7753 (t80) REVERT: I 1 MET cc_start: 0.7100 (mmm) cc_final: 0.6842 (tpt) REVERT: I 30 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7667 (mmt180) REVERT: I 130 ASP cc_start: 0.7613 (m-30) cc_final: 0.7346 (m-30) REVERT: G 342 LYS cc_start: 0.8843 (tttt) cc_final: 0.8524 (tmmt) REVERT: H 321 ARG cc_start: 0.8526 (ttp80) cc_final: 0.8158 (mtp-110) outliers start: 136 outliers final: 88 residues processed: 488 average time/residue: 0.1712 time to fit residues: 132.7616 Evaluate side-chains 441 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 347 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 541 HIS Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 568 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 466 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 193 optimal weight: 0.6980 chunk 205 optimal weight: 0.0010 chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 chunk 256 optimal weight: 0.0870 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 HIS B 226 ASN B 280 ASN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.195266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.152512 restraints weight = 30768.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150043 restraints weight = 25821.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153196 restraints weight = 23366.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153961 restraints weight = 14639.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155695 restraints weight = 13420.382| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25158 Z= 0.129 Angle : 0.571 12.088 34151 Z= 0.296 Chirality : 0.041 0.276 3720 Planarity : 0.004 0.063 4381 Dihedral : 5.685 57.436 3372 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.62 % Allowed : 19.73 % Favored : 76.65 % 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: 0.31 (0.15), residues: 3040 helix: 1.34 (0.13), residues: 1526 sheet: -1.57 (0.26), residues: 397 loop : -0.59 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 343 TYR 0.028 0.002 TYR H 332 PHE 0.018 0.002 PHE C 63 TRP 0.024 0.001 TRP B 143 HIS 0.017 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00286 (25158) covalent geometry : angle 0.57100 (34151) hydrogen bonds : bond 0.04036 ( 1169) hydrogen bonds : angle 4.92496 ( 3402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 391 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7333 (m) cc_final: 0.7070 (t) REVERT: J 95 TYR cc_start: 0.7268 (m-80) cc_final: 0.6624 (m-80) REVERT: J 115 PHE cc_start: 0.6459 (m-10) cc_final: 0.5856 (m-10) REVERT: B 94 MET cc_start: 0.2580 (mmp) cc_final: 0.1806 (mmm) REVERT: B 351 TYR cc_start: 0.6717 (t80) cc_final: 0.6464 (m-80) REVERT: B 419 MET cc_start: 0.8166 (mmp) cc_final: 0.7649 (mmp) REVERT: B 542 ILE cc_start: 0.6117 (mm) cc_final: 0.4771 (pt) REVERT: B 567 LEU cc_start: 0.7124 (tp) cc_final: 0.6550 (tt) REVERT: C 30 PHE cc_start: 0.8119 (m-10) cc_final: 0.7897 (m-80) REVERT: C 132 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: C 236 ARG cc_start: 0.7260 (mtp85) cc_final: 0.7032 (mtt-85) REVERT: C 243 CYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6466 (m) REVERT: C 277 VAL cc_start: 0.8750 (t) cc_final: 0.8491 (m) REVERT: C 538 MET cc_start: 0.8724 (mmt) cc_final: 0.8520 (mmt) REVERT: C 615 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7887 (ttmt) REVERT: D 592 LEU cc_start: 0.8655 (tp) cc_final: 0.8315 (tp) REVERT: A 100 LYS cc_start: 0.6923 (mtmp) cc_final: 0.6037 (mttp) REVERT: A 102 TYR cc_start: 0.7437 (m-80) cc_final: 0.7065 (m-10) REVERT: A 509 TYR cc_start: 0.7833 (t80) cc_final: 0.7624 (t80) REVERT: A 526 SER cc_start: 0.8552 (p) cc_final: 0.8233 (m) REVERT: A 572 TYR cc_start: 0.7706 (t80) cc_final: 0.7345 (t80) REVERT: I 1 MET cc_start: 0.7071 (mmm) cc_final: 0.6856 (tpt) REVERT: I 30 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7646 (mmt180) REVERT: I 130 ASP cc_start: 0.7438 (m-30) cc_final: 0.7175 (m-30) REVERT: G 342 LYS cc_start: 0.8853 (tttt) cc_final: 0.8623 (tttm) REVERT: H 321 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8120 (mtp-110) outliers start: 94 outliers final: 62 residues processed: 460 average time/residue: 0.1659 time to fit residues: 121.7674 Evaluate side-chains 419 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 355 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 378 GLU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 221 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 HIS ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.192514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148469 restraints weight = 31157.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148019 restraints weight = 23314.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149212 restraints weight = 25582.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.152098 restraints weight = 15955.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.152799 restraints weight = 12452.162| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25158 Z= 0.183 Angle : 0.592 12.532 34151 Z= 0.307 Chirality : 0.043 0.270 3720 Planarity : 0.004 0.062 4381 Dihedral : 5.572 54.010 3371 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.08 % Allowed : 19.92 % Favored : 76.00 % 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: 0.23 (0.15), residues: 3040 helix: 1.28 (0.13), residues: 1527 sheet: -1.63 (0.26), residues: 382 loop : -0.65 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 211 TYR 0.045 0.002 TYR B 548 PHE 0.021 0.002 PHE D 312 TRP 0.027 0.002 TRP J 174 HIS 0.005 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00430 (25158) covalent geometry : angle 0.59165 (34151) hydrogen bonds : bond 0.04033 ( 1169) hydrogen bonds : angle 4.91624 ( 3402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 366 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7137 (m) cc_final: 0.6905 (t) REVERT: J 95 TYR cc_start: 0.7310 (m-80) cc_final: 0.6701 (m-80) REVERT: B 351 TYR cc_start: 0.6770 (t80) cc_final: 0.6451 (m-80) REVERT: B 419 MET cc_start: 0.8173 (mmp) cc_final: 0.7669 (mmp) REVERT: B 538 MET cc_start: 0.5625 (OUTLIER) cc_final: 0.5388 (tpt) REVERT: B 542 ILE cc_start: 0.6046 (mm) cc_final: 0.4736 (pt) REVERT: C 243 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6431 (m) REVERT: C 450 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7114 (p0) REVERT: C 615 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7940 (ttmt) REVERT: D 100 LYS cc_start: 0.7700 (mttt) cc_final: 0.7314 (tptt) REVERT: D 180 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.7801 (m90) REVERT: D 336 ASN cc_start: 0.8052 (m-40) cc_final: 0.7701 (m-40) REVERT: D 581 GLN cc_start: 0.7664 (mt0) cc_final: 0.7340 (mt0) REVERT: D 592 LEU cc_start: 0.8726 (tp) cc_final: 0.8467 (tp) REVERT: A 52 LYS cc_start: 0.6663 (tmmt) cc_final: 0.6281 (ttmt) REVERT: A 100 LYS cc_start: 0.6888 (mtmp) cc_final: 0.5939 (mttp) REVERT: A 102 TYR cc_start: 0.7470 (m-80) cc_final: 0.6997 (m-10) REVERT: A 295 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7362 (t0) REVERT: A 509 TYR cc_start: 0.7943 (t80) cc_final: 0.7606 (t80) REVERT: A 526 SER cc_start: 0.8620 (p) cc_final: 0.8304 (m) REVERT: A 572 TYR cc_start: 0.7695 (t80) cc_final: 0.7420 (t80) REVERT: I 1 MET cc_start: 0.7063 (mmm) cc_final: 0.6845 (tpt) REVERT: I 30 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7690 (mmt180) REVERT: I 130 ASP cc_start: 0.7518 (m-30) cc_final: 0.7287 (m-30) REVERT: G 342 LYS cc_start: 0.8790 (tttt) cc_final: 0.8577 (tttm) REVERT: H 321 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8078 (mtp-110) outliers start: 106 outliers final: 79 residues processed: 446 average time/residue: 0.1692 time to fit residues: 120.5094 Evaluate side-chains 430 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 346 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 180 HIS Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 378 GLU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 15 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 243 optimal weight: 6.9990 chunk 303 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 273 optimal weight: 0.9980 chunk 72 optimal weight: 0.0670 chunk 172 optimal weight: 0.5980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 242 HIS ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS D 180 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN I 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.196743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.154775 restraints weight = 30967.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152770 restraints weight = 26193.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156174 restraints weight = 22929.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156570 restraints weight = 14620.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.158210 restraints weight = 13602.925| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25158 Z= 0.124 Angle : 0.553 11.644 34151 Z= 0.285 Chirality : 0.041 0.278 3720 Planarity : 0.004 0.071 4381 Dihedral : 5.412 55.514 3369 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.35 % Allowed : 20.08 % Favored : 76.58 % 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: 0.36 (0.15), residues: 3040 helix: 1.37 (0.13), residues: 1538 sheet: -1.54 (0.26), residues: 390 loop : -0.60 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 343 TYR 0.049 0.002 TYR B 548 PHE 0.019 0.001 PHE J 115 TRP 0.032 0.001 TRP J 174 HIS 0.021 0.001 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00278 (25158) covalent geometry : angle 0.55264 (34151) hydrogen bonds : bond 0.03771 ( 1169) hydrogen bonds : angle 4.76162 ( 3402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 371 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7223 (m-80) cc_final: 0.6634 (m-80) REVERT: B 424 ASP cc_start: 0.7636 (p0) cc_final: 0.7381 (p0) REVERT: B 542 ILE cc_start: 0.6001 (mm) cc_final: 0.4766 (pt) REVERT: B 600 TYR cc_start: 0.6179 (t80) cc_final: 0.5627 (t80) REVERT: C 315 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7805 (m170) REVERT: C 419 MET cc_start: 0.7958 (mmt) cc_final: 0.7591 (mmt) REVERT: C 615 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7976 (ttmt) REVERT: D 100 LYS cc_start: 0.7684 (mttt) cc_final: 0.7293 (tptt) REVERT: D 336 ASN cc_start: 0.7972 (m-40) cc_final: 0.7626 (m-40) REVERT: D 539 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6765 (mt-10) REVERT: D 592 LEU cc_start: 0.8718 (tp) cc_final: 0.8428 (tp) REVERT: A 52 LYS cc_start: 0.6691 (tmmt) cc_final: 0.6330 (ttmt) REVERT: A 81 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6923 (tm-30) REVERT: A 100 LYS cc_start: 0.6872 (mtmp) cc_final: 0.5905 (mttp) REVERT: A 102 TYR cc_start: 0.7422 (m-80) cc_final: 0.7026 (m-10) REVERT: A 509 TYR cc_start: 0.7750 (t80) cc_final: 0.7479 (t80) REVERT: A 526 SER cc_start: 0.8586 (p) cc_final: 0.8269 (m) REVERT: E 342 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8192 (ttpp) REVERT: I 1 MET cc_start: 0.7063 (mmm) cc_final: 0.6860 (tpt) REVERT: I 30 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7691 (mmt180) REVERT: H 321 ARG cc_start: 0.8436 (ttp80) cc_final: 0.8085 (mtp-110) outliers start: 87 outliers final: 71 residues processed: 437 average time/residue: 0.1684 time to fit residues: 117.0709 Evaluate side-chains 422 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 349 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 261 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 43 optimal weight: 0.0570 chunk 12 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 195 optimal weight: 0.4980 chunk 300 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 230 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS E 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.194003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151862 restraints weight = 31157.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150853 restraints weight = 24299.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152350 restraints weight = 26169.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154409 restraints weight = 16483.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.155639 restraints weight = 13628.362| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25158 Z= 0.174 Angle : 0.577 12.192 34151 Z= 0.299 Chirality : 0.042 0.271 3720 Planarity : 0.004 0.070 4381 Dihedral : 5.402 56.652 3368 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.58 % Allowed : 19.96 % Favored : 76.46 % 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: 0.29 (0.15), residues: 3040 helix: 1.32 (0.13), residues: 1536 sheet: -1.62 (0.26), residues: 384 loop : -0.61 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 211 TYR 0.032 0.002 TYR B 548 PHE 0.020 0.002 PHE D 312 TRP 0.037 0.002 TRP J 174 HIS 0.004 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00410 (25158) covalent geometry : angle 0.57712 (34151) hydrogen bonds : bond 0.03872 ( 1169) hydrogen bonds : angle 4.79682 ( 3402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 357 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7235 (m-80) cc_final: 0.6652 (m-80) REVERT: B 542 ILE cc_start: 0.6126 (mm) cc_final: 0.4908 (pt) REVERT: C 227 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.6931 (m-80) REVERT: C 315 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7965 (m170) REVERT: C 450 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.6964 (p0) REVERT: C 595 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8064 (tt) REVERT: C 615 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7960 (ttmt) REVERT: D 100 LYS cc_start: 0.7623 (mttt) cc_final: 0.7262 (tptt) REVERT: D 236 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7655 (mmt90) REVERT: D 336 ASN cc_start: 0.8046 (m-40) cc_final: 0.7699 (m-40) REVERT: A 52 LYS cc_start: 0.6855 (tmmt) cc_final: 0.6587 (ttmt) REVERT: A 100 LYS cc_start: 0.6893 (mtmp) cc_final: 0.5866 (mttp) REVERT: A 102 TYR cc_start: 0.7485 (m-80) cc_final: 0.7046 (m-10) REVERT: A 526 SER cc_start: 0.8587 (p) cc_final: 0.8278 (m) REVERT: E 342 LYS cc_start: 0.8468 (ttpt) cc_final: 0.8259 (ttmm) REVERT: I 30 ARG cc_start: 0.8205 (mtm-85) cc_final: 0.7714 (mmt180) REVERT: I 130 ASP cc_start: 0.7650 (m-30) cc_final: 0.7417 (m-30) REVERT: H 321 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8070 (mtp-110) outliers start: 93 outliers final: 79 residues processed: 434 average time/residue: 0.1633 time to fit residues: 112.7100 Evaluate side-chains 420 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 337 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 135 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 181 optimal weight: 0.8980 chunk 278 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 245 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.195716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.153256 restraints weight = 31196.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152886 restraints weight = 22997.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154373 restraints weight = 24628.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.155971 restraints weight = 15920.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157233 restraints weight = 13587.100| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25158 Z= 0.143 Angle : 0.575 12.062 34151 Z= 0.296 Chirality : 0.042 0.298 3720 Planarity : 0.004 0.070 4381 Dihedral : 5.381 58.589 3368 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.58 % Allowed : 20.38 % Favored : 76.04 % 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 (0.15), residues: 3040 helix: 1.33 (0.13), residues: 1539 sheet: -1.59 (0.26), residues: 384 loop : -0.60 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 343 TYR 0.038 0.002 TYR C 68 PHE 0.016 0.001 PHE A 481 TRP 0.053 0.002 TRP J 174 HIS 0.004 0.001 HIS J 151 Details of bonding type rmsd covalent geometry : bond 0.00331 (25158) covalent geometry : angle 0.57541 (34151) hydrogen bonds : bond 0.03735 ( 1169) hydrogen bonds : angle 4.74130 ( 3402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 345 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7202 (m-80) cc_final: 0.6597 (m-80) REVERT: B 542 ILE cc_start: 0.6027 (mm) cc_final: 0.4801 (pt) REVERT: C 211 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.8085 (ttm110) REVERT: C 227 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.6860 (m-80) REVERT: C 242 TYR cc_start: 0.8084 (OUTLIER) cc_final: 0.7701 (t80) REVERT: C 315 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7926 (m170) REVERT: C 419 MET cc_start: 0.7898 (mmt) cc_final: 0.7612 (mmt) REVERT: C 450 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.6960 (p0) REVERT: C 615 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7920 (ttmt) REVERT: D 100 LYS cc_start: 0.7633 (mttt) cc_final: 0.7245 (tptt) REVERT: D 236 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7610 (mmt90) REVERT: D 336 ASN cc_start: 0.8015 (m-40) cc_final: 0.7682 (m-40) REVERT: A 52 LYS cc_start: 0.6852 (tmmt) cc_final: 0.6495 (ttmt) REVERT: A 100 LYS cc_start: 0.6817 (mtmp) cc_final: 0.5798 (mttp) REVERT: A 102 TYR cc_start: 0.7457 (m-80) cc_final: 0.7058 (m-10) REVERT: A 620 HIS cc_start: 0.7114 (t70) cc_final: 0.6536 (t-90) REVERT: E 342 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8259 (ttmm) REVERT: I 30 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7706 (mmt180) REVERT: I 130 ASP cc_start: 0.7705 (m-30) cc_final: 0.7452 (m-30) REVERT: G 343 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7329 (mtm110) REVERT: H 321 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7999 (mtp-110) outliers start: 93 outliers final: 80 residues processed: 424 average time/residue: 0.1573 time to fit residues: 106.2517 Evaluate side-chains 415 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 331 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 297 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 59 optimal weight: 10.0000 chunk 243 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 255 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.196528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154575 restraints weight = 31148.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154424 restraints weight = 22698.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155479 restraints weight = 25802.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157765 restraints weight = 16112.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158927 restraints weight = 12992.823| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25158 Z= 0.137 Angle : 0.583 15.361 34151 Z= 0.297 Chirality : 0.042 0.308 3720 Planarity : 0.004 0.071 4381 Dihedral : 5.324 59.529 3368 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.31 % Allowed : 21.04 % Favored : 75.65 % 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: 0.36 (0.15), residues: 3040 helix: 1.35 (0.13), residues: 1543 sheet: -1.54 (0.26), residues: 382 loop : -0.57 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 236 TYR 0.031 0.002 TYR B 351 PHE 0.016 0.001 PHE D 312 TRP 0.049 0.002 TRP J 174 HIS 0.015 0.001 HIS I 151 Details of bonding type rmsd covalent geometry : bond 0.00318 (25158) covalent geometry : angle 0.58339 (34151) hydrogen bonds : bond 0.03717 ( 1169) hydrogen bonds : angle 4.70652 ( 3402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 353 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7087 (m-80) cc_final: 0.6523 (m-80) REVERT: B 94 MET cc_start: 0.2804 (mmp) cc_final: 0.2195 (mmt) REVERT: B 221 TYR cc_start: 0.5231 (m-80) cc_final: 0.5001 (m-80) REVERT: B 492 ASP cc_start: 0.6730 (t0) cc_final: 0.6129 (p0) REVERT: B 542 ILE cc_start: 0.5959 (mm) cc_final: 0.4772 (pt) REVERT: B 600 TYR cc_start: 0.6800 (t80) cc_final: 0.5995 (t80) REVERT: C 227 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: C 242 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7652 (t80) REVERT: C 315 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7819 (m170) REVERT: C 419 MET cc_start: 0.7832 (mmt) cc_final: 0.7503 (mmt) REVERT: C 450 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.6983 (p0) REVERT: C 615 LYS cc_start: 0.8144 (mmtm) cc_final: 0.7863 (ttmt) REVERT: D 100 LYS cc_start: 0.7635 (mttt) cc_final: 0.7290 (tptt) REVERT: D 134 TRP cc_start: 0.8762 (t-100) cc_final: 0.8489 (t-100) REVERT: D 236 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7603 (mmt90) REVERT: D 336 ASN cc_start: 0.8002 (m-40) cc_final: 0.7669 (m-40) REVERT: D 415 ASP cc_start: 0.7568 (t0) cc_final: 0.7291 (t0) REVERT: A 52 LYS cc_start: 0.6781 (tmmt) cc_final: 0.6468 (ttmt) REVERT: A 100 LYS cc_start: 0.6888 (mtmp) cc_final: 0.5890 (mttp) REVERT: A 102 TYR cc_start: 0.7465 (m-80) cc_final: 0.7145 (m-10) REVERT: A 620 HIS cc_start: 0.7079 (t70) cc_final: 0.6642 (t-170) REVERT: E 342 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8245 (ttmm) REVERT: I 30 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7704 (mmt180) REVERT: I 130 ASP cc_start: 0.7659 (m-30) cc_final: 0.7425 (m-30) REVERT: G 343 ARG cc_start: 0.7411 (mtm110) cc_final: 0.7159 (mtm110) REVERT: H 321 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8143 (mtp-110) outliers start: 86 outliers final: 77 residues processed: 427 average time/residue: 0.1605 time to fit residues: 109.0539 Evaluate side-chains 418 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 337 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 242 TYR Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 HIS Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 403 LYS Chi-restraints excluded: chain C residue 416 MET Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 425 PHE Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 194 ILE Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 317 SER Chi-restraints excluded: chain F residue 348 TYR Chi-restraints excluded: chain H residue 348 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 243 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 183 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 198 optimal weight: 0.0470 chunk 225 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.197338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155412 restraints weight = 31035.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153844 restraints weight = 25622.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157175 restraints weight = 22568.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157490 restraints weight = 14242.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159178 restraints weight = 13312.467| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25158 Z= 0.129 Angle : 0.569 14.092 34151 Z= 0.291 Chirality : 0.041 0.315 3720 Planarity : 0.004 0.067 4381 Dihedral : 5.249 57.164 3367 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.08 % Allowed : 21.35 % Favored : 75.58 % 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 (0.15), residues: 3040 helix: 1.40 (0.13), residues: 1541 sheet: -1.51 (0.26), residues: 377 loop : -0.57 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 343 TYR 0.033 0.002 TYR C 68 PHE 0.017 0.001 PHE A 481 TRP 0.045 0.002 TRP J 174 HIS 0.015 0.001 HIS I 151 Details of bonding type rmsd covalent geometry : bond 0.00300 (25158) covalent geometry : angle 0.56937 (34151) hydrogen bonds : bond 0.03633 ( 1169) hydrogen bonds : angle 4.65423 ( 3402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.56 seconds wall clock time: 72 minutes 56.48 seconds (4376.48 seconds total)