Starting phenix.real_space_refine on Sat Jun 21 04:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cvz_27022/06_2025/8cvz_27022.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cvz_27022/06_2025/8cvz_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_27022/06_2025/8cvz_27022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cvz_27022/06_2025/8cvz_27022.map" model { file = "/net/cci-nas-00/data/ceres_data/8cvz_27022/06_2025/8cvz_27022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cvz_27022/06_2025/8cvz_27022.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 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, 'ASN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG: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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLU:plan': 3, 'ASP:plan': 1} 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, 'ARG:plan': 1, 'ASP:plan': 2} 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: 15.31, per 1000 atoms: 0.62 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: 6.56 Conformation dependent library (CDL) restraints added in 3.4 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: 2.95 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: 9.53 Time building geometry restraints manager: 7.80 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 59.120 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.630 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (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 TRP 0.064 0.009 TRP C 34 HIS 0.026 0.007 HIS B 297 PHE 0.073 0.009 PHE B 154 TYR 0.081 0.008 TYR C 572 ARG 0.024 0.003 ARG D 555 Details of bonding type rmsd hydrogen bonds : bond 0.19587 ( 1169) hydrogen bonds : angle 7.25412 ( 3402) covalent geometry : bond 0.00819 (25158) covalent geometry : angle 1.57373 (34151) *********************** 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 : 2.854 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: 0.5770 (pp) REVERT: B 116 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.4247 (tp) REVERT: B 171 GLU cc_start: 0.2827 (OUTLIER) cc_final: 0.2441 (tp30) REVERT: B 292 GLU cc_start: 0.1888 (OUTLIER) cc_final: -0.0227 (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: 0.7380 (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: 0.6620 (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: 0.6721 (tp30) REVERT: D 337 LYS cc_start: 0.8327 (mptp) cc_final: 0.8024 (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: 0.6894 (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: 0.5982 (t) REVERT: E 317 SER cc_start: 0.6859 (OUTLIER) cc_final: 0.6293 (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: 0.8271 (tm-30) REVERT: H 316 VAL cc_start: 0.2848 (OUTLIER) cc_final: 0.2581 (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: 0.4680 time to fit residues: 588.8995 Evaluate side-chains 509 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 447 time to evaluate : 2.593 ------------------------------------------------------------------------------- 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 256 optimal weight: 0.8980 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 276 optimal weight: 7.9990 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 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 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN B 541 HIS B 581 GLN B 587 ASN C 178 HIS 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 D 436 GLN D 576 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 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: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154050 restraints weight = 30734.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154731 restraints weight = 22102.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156423 restraints weight = 21708.156| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2842 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 : 0.638 9.460 34151 Z= 0.342 Chirality : 0.044 0.207 3720 Planarity : 0.004 0.057 4381 Dihedral : 7.464 71.460 3449 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.65 % Allowed : 15.69 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.15), residues: 3040 helix: 1.56 (0.13), residues: 1531 sheet: -1.20 (0.26), residues: 383 loop : -0.63 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 34 HIS 0.009 0.001 HIS C 240 PHE 0.028 0.002 PHE C 156 TYR 0.021 0.002 TYR D 572 ARG 0.008 0.001 ARG B 498 Details of bonding type rmsd hydrogen bonds : bond 0.05269 ( 1169) hydrogen bonds : angle 5.36924 ( 3402) covalent geometry : bond 0.00364 (25158) covalent geometry : angle 0.63819 (34151) *********************** 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 593 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 472 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7832 (m) cc_final: 0.7547 (t) REVERT: J 95 TYR cc_start: 0.7318 (m-80) cc_final: 0.6599 (m-80) REVERT: J 125 ASP cc_start: 0.8547 (t0) cc_final: 0.8195 (t0) REVERT: B 292 GLU cc_start: 0.1765 (OUTLIER) cc_final: 0.0950 (tp30) REVERT: B 319 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8012 (m-40) REVERT: B 424 ASP cc_start: 0.7394 (p0) cc_final: 0.7093 (p0) REVERT: B 548 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.5102 (t80) REVERT: C 24 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6169 (pp) REVERT: C 204 THR cc_start: 0.8988 (p) cc_final: 0.8747 (t) REVERT: C 212 TYR cc_start: 0.7740 (m-80) cc_final: 0.7395 (m-10) REVERT: C 331 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8111 (mtm110) REVERT: C 606 MET cc_start: 0.6492 (mtm) cc_final: 0.6288 (mtm) REVERT: D 100 LYS cc_start: 0.7830 (mttt) cc_final: 0.7196 (tptt) REVERT: D 174 HIS cc_start: 0.6492 (m-70) cc_final: 0.6086 (m90) REVERT: D 236 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7582 (mmt90) REVERT: D 387 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8419 (tptt) REVERT: D 419 MET cc_start: 0.7576 (mmp) cc_final: 0.7375 (mmp) REVERT: D 522 MET cc_start: 0.8577 (mtp) cc_final: 0.8314 (mtt) REVERT: D 611 MET cc_start: 0.6895 (mmm) cc_final: 0.6570 (mtt) REVERT: A 35 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: A 68 TYR cc_start: 0.7406 (t80) cc_final: 0.7156 (t80) REVERT: A 100 LYS cc_start: 0.6914 (mtmp) cc_final: 0.6105 (mtmm) REVERT: A 102 TYR cc_start: 0.7592 (m-80) cc_final: 0.7156 (m-10) REVERT: A 466 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: A 572 TYR cc_start: 0.7518 (t80) cc_final: 0.7289 (t80) REVERT: A 586 ARG cc_start: 0.6968 (mmm160) cc_final: 0.6741 (tpp80) REVERT: E 333 MET cc_start: 0.8466 (mmm) cc_final: 0.8003 (mtt) REVERT: I 30 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7313 (mmt180) outliers start: 121 outliers final: 58 residues processed: 560 average time/residue: 0.4295 time to fit residues: 376.8417 Evaluate side-chains 445 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 380 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 24 SER 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 421 ASP 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 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 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 115 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 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 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 E residue 348 TYR 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 107 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 131 optimal weight: 0.0670 chunk 145 optimal weight: 0.0970 chunk 170 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- 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 222 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 180 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.192045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147863 restraints weight = 30851.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147168 restraints weight = 22967.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148507 restraints weight = 24933.836| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25158 Z= 0.194 Angle : 0.630 14.280 34151 Z= 0.330 Chirality : 0.045 0.245 3720 Planarity : 0.004 0.082 4381 Dihedral : 6.439 71.100 3391 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.50 % Allowed : 16.65 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3040 helix: 1.41 (0.13), residues: 1529 sheet: -1.46 (0.25), residues: 399 loop : -0.61 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 34 HIS 0.012 0.001 HIS A 178 PHE 0.039 0.002 PHE D 312 TYR 0.030 0.002 TYR H 332 ARG 0.011 0.001 ARG D 437 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 1169) hydrogen bonds : angle 5.16198 ( 3402) covalent geometry : bond 0.00451 (25158) covalent geometry : angle 0.63050 (34151) *********************** 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 529 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 412 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7723 (m) cc_final: 0.7249 (t) REVERT: J 95 TYR cc_start: 0.7430 (m-80) cc_final: 0.6722 (m-80) REVERT: J 125 ASP cc_start: 0.8578 (t70) cc_final: 0.8128 (t0) REVERT: B 94 MET cc_start: 0.1773 (mmp) cc_final: 0.0899 (mmt) REVERT: B 319 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: B 390 TRP cc_start: 0.8149 (t-100) cc_final: 0.7755 (t60) REVERT: B 416 MET cc_start: 0.7879 (mmm) cc_final: 0.7557 (mmm) REVERT: B 419 MET cc_start: 0.7966 (mmt) cc_final: 0.7675 (mmp) REVERT: B 538 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.5017 (mmt) REVERT: B 542 ILE cc_start: 0.6110 (mm) cc_final: 0.4698 (pt) REVERT: B 548 TYR cc_start: 0.5498 (OUTLIER) cc_final: 0.5249 (t80) REVERT: B 578 SER cc_start: 0.7710 (OUTLIER) cc_final: 0.7489 (p) REVERT: C 204 THR cc_start: 0.9065 (p) cc_final: 0.8786 (t) REVERT: C 277 VAL cc_start: 0.8801 (t) cc_final: 0.8449 (m) REVERT: C 331 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8204 (mtm110) REVERT: C 538 MET cc_start: 0.8775 (mmm) cc_final: 0.8421 (mmt) REVERT: C 552 ILE cc_start: 0.9084 (mm) cc_final: 0.8849 (mm) REVERT: C 615 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7924 (ttmt) REVERT: D 236 ARG cc_start: 0.7967 (mmt90) cc_final: 0.7676 (mmt90) REVERT: D 415 ASP cc_start: 0.7498 (t0) cc_final: 0.7191 (t0) REVERT: D 419 MET cc_start: 0.7495 (mmp) cc_final: 0.7223 (mmp) REVERT: D 427 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7289 (ttm) REVERT: D 522 MET cc_start: 0.8535 (mtp) cc_final: 0.8307 (mtt) REVERT: A 35 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: A 43 ILE cc_start: 0.8962 (mt) cc_final: 0.8391 (mt) REVERT: A 70 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 94 MET cc_start: 0.7449 (mmm) cc_final: 0.7224 (ttm) REVERT: A 100 LYS cc_start: 0.6994 (mtmp) cc_final: 0.6179 (mtmm) REVERT: A 102 TYR cc_start: 0.7539 (m-80) cc_final: 0.7161 (m-10) REVERT: A 586 ARG cc_start: 0.6977 (mmm160) cc_final: 0.6725 (tpp80) REVERT: E 333 MET cc_start: 0.8496 (mmm) cc_final: 0.7998 (mtt) REVERT: I 30 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7395 (mmt-90) REVERT: G 342 LYS cc_start: 0.8815 (tttm) cc_final: 0.8526 (tttm) REVERT: H 321 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8058 (mtp-110) outliers start: 117 outliers final: 74 residues processed: 493 average time/residue: 0.4442 time to fit residues: 349.4119 Evaluate side-chains 444 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 362 time to evaluate : 2.464 ------------------------------------------------------------------------------- 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 34 TRP 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 538 MET Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 578 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 188 LEU Chi-restraints excluded: chain C residue 259 SER 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 D residue 36 VAL Chi-restraints excluded: chain D residue 115 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 229 VAL 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 372 THR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 457 LEU 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 70 GLU 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 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 361 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 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 E residue 348 TYR 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 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 317 SER 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 168 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN A 95 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.193420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150834 restraints weight = 31050.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.148922 restraints weight = 24566.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150296 restraints weight = 27680.011| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25158 Z= 0.184 Angle : 0.590 12.017 34151 Z= 0.308 Chirality : 0.043 0.225 3720 Planarity : 0.004 0.065 4381 Dihedral : 5.934 56.314 3379 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.69 % Allowed : 17.58 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 3040 helix: 1.39 (0.13), residues: 1530 sheet: -1.50 (0.26), residues: 400 loop : -0.54 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 106 HIS 0.008 0.001 HIS C 610 PHE 0.024 0.002 PHE B 375 TYR 0.027 0.002 TYR A 313 ARG 0.010 0.001 ARG J 48 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1169) hydrogen bonds : angle 5.00308 ( 3402) covalent geometry : bond 0.00428 (25158) covalent geometry : angle 0.59041 (34151) *********************** 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 513 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 391 time to evaluate : 2.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 SER cc_start: 0.7774 (m) cc_final: 0.7477 (t) REVERT: J 95 TYR cc_start: 0.7318 (m-80) cc_final: 0.6668 (m-80) REVERT: B 94 MET cc_start: 0.2129 (mmp) cc_final: 0.1517 (mmt) REVERT: B 351 TYR cc_start: 0.6788 (t80) cc_final: 0.6444 (m-80) REVERT: B 374 ASN cc_start: 0.7469 (t0) cc_final: 0.7227 (t0) REVERT: B 390 TRP cc_start: 0.8238 (t-100) cc_final: 0.7800 (t60) REVERT: B 494 GLU cc_start: 0.6554 (tt0) cc_final: 0.6285 (mp0) REVERT: B 528 SER cc_start: 0.7343 (OUTLIER) cc_final: 0.6836 (t) REVERT: B 542 ILE cc_start: 0.6363 (mm) cc_final: 0.5016 (pt) REVERT: B 588 ARG cc_start: 0.6427 (mmt-90) cc_final: 0.6182 (mmt-90) REVERT: C 243 CYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6536 (m) REVERT: C 277 VAL cc_start: 0.8853 (t) cc_final: 0.8560 (m) REVERT: C 331 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (mtm110) REVERT: C 524 ILE cc_start: 0.9185 (mm) cc_final: 0.8914 (mm) REVERT: C 528 SER cc_start: 0.8652 (t) cc_final: 0.8387 (m) REVERT: C 595 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8187 (tt) REVERT: C 615 LYS cc_start: 0.8233 (mmtm) cc_final: 0.7834 (ttmt) REVERT: D 147 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7713 (mm-30) REVERT: D 180 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.8056 (m170) REVERT: D 236 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7552 (mmt90) REVERT: A 94 MET cc_start: 0.7603 (mmm) cc_final: 0.7140 (ttm) REVERT: A 100 LYS cc_start: 0.6965 (mtmp) cc_final: 0.6262 (mttp) REVERT: A 466 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: A 579 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7748 (tpt90) REVERT: A 586 ARG cc_start: 0.7098 (mmm160) cc_final: 0.6858 (tpp80) REVERT: I 30 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7614 (mmt180) REVERT: I 47 MET cc_start: 0.8423 (tpp) cc_final: 0.8124 (tpp) REVERT: I 60 MET cc_start: 0.8171 (tpp) cc_final: 0.7945 (tpp) REVERT: I 130 ASP cc_start: 0.7414 (m-30) cc_final: 0.7213 (m-30) outliers start: 122 outliers final: 77 residues processed: 484 average time/residue: 0.3693 time to fit residues: 285.9959 Evaluate side-chains 446 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 362 time to evaluate : 3.387 ------------------------------------------------------------------------------- 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 120 LEU 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 129 TRP 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 528 SER Chi-restraints excluded: chain B residue 538 MET 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 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 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 115 VAL Chi-restraints excluded: chain D residue 152 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 316 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 335 SER 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 484 SER Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain D residue 589 THR 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 115 VAL 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 214 CYS 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 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 579 ARG 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 E residue 337 SER Chi-restraints excluded: chain E residue 348 TYR 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 176 THR Chi-restraints excluded: chain I residue 190 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 85 optimal weight: 0.0070 chunk 257 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- 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 178 HIS B 226 ASN C 149 ASN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.193475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150585 restraints weight = 31077.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149502 restraints weight = 24195.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.151097 restraints weight = 26514.750| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25158 Z= 0.164 Angle : 0.579 12.249 34151 Z= 0.300 Chirality : 0.042 0.248 3720 Planarity : 0.004 0.062 4381 Dihedral : 5.746 55.040 3376 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.62 % Allowed : 18.88 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3040 helix: 1.38 (0.13), residues: 1522 sheet: -1.57 (0.26), residues: 397 loop : -0.62 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 106 HIS 0.006 0.001 HIS C 610 PHE 0.027 0.002 PHE C 63 TYR 0.032 0.002 TYR H 332 ARG 0.009 0.000 ARG G 343 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 1169) hydrogen bonds : angle 4.93313 ( 3402) covalent geometry : bond 0.00379 (25158) covalent geometry : angle 0.57879 (34151) *********************** 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 495 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 375 time to evaluate : 2.751 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: 0.7272 (m) cc_final: 0.7035 (t) REVERT: J 48 ARG cc_start: 0.7497 (mpt-90) cc_final: 0.7243 (mpt-90) REVERT: J 95 TYR cc_start: 0.7288 (m-80) cc_final: 0.6610 (m-80) REVERT: B 94 MET cc_start: 0.2265 (mmp) cc_final: 0.1745 (mmt) REVERT: B 351 TYR cc_start: 0.6757 (t80) cc_final: 0.6460 (m-80) REVERT: B 390 TRP cc_start: 0.8261 (t-100) cc_final: 0.8028 (t-100) REVERT: B 419 MET cc_start: 0.8011 (mmt) cc_final: 0.7748 (mmp) REVERT: B 421 ASP cc_start: 0.6926 (p0) cc_final: 0.6665 (p0) REVERT: B 424 ASP cc_start: 0.7543 (p0) cc_final: 0.7332 (p0) REVERT: B 494 GLU cc_start: 0.6584 (tt0) cc_final: 0.6323 (mp0) REVERT: B 528 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.6536 (t) REVERT: B 542 ILE cc_start: 0.6320 (mm) cc_final: 0.5036 (pt) REVERT: B 567 LEU cc_start: 0.7131 (tp) cc_final: 0.6562 (tt) REVERT: C 236 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7017 (mtt-85) REVERT: C 243 CYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6548 (m) REVERT: C 277 VAL cc_start: 0.8825 (t) cc_final: 0.8598 (m) REVERT: C 450 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.6994 (p0) REVERT: C 528 SER cc_start: 0.8636 (t) cc_final: 0.8359 (m) REVERT: C 595 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8082 (tt) REVERT: C 615 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7929 (ttmt) REVERT: D 57 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7423 (tm-30) REVERT: D 180 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8017 (m170) REVERT: D 236 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7568 (mmt90) REVERT: A 81 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6952 (tm-30) REVERT: A 94 MET cc_start: 0.7644 (mmm) cc_final: 0.7074 (ttm) REVERT: A 100 LYS cc_start: 0.7199 (mtmp) cc_final: 0.6464 (mttp) REVERT: A 295 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7260 (t0) REVERT: A 572 TYR cc_start: 0.7678 (t80) cc_final: 0.7470 (t80) REVERT: A 579 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7777 (tpt90) REVERT: I 1 MET cc_start: 0.7087 (mmm) cc_final: 0.6865 (tpt) REVERT: I 30 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7638 (mmt180) REVERT: I 47 MET cc_start: 0.8375 (tpp) cc_final: 0.8048 (tpp) REVERT: I 52 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7169 (tp30) REVERT: I 130 ASP cc_start: 0.7497 (m-30) cc_final: 0.7183 (m-30) REVERT: H 333 MET cc_start: 0.7955 (mtt) cc_final: 0.7643 (pmm) outliers start: 120 outliers final: 86 residues processed: 470 average time/residue: 0.3644 time to fit residues: 273.7963 Evaluate side-chains 444 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 351 time to evaluate : 2.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 LEU 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 34 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 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 425 PHE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 528 SER 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 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 162 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 323 THR Chi-restraints excluded: chain C residue 350 ASN 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 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 VAL 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 186 VAL 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 362 VAL 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 520 THR 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 207 THR 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 295 ASN 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 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 579 ARG Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 80 LEU 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 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 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 275 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 202 optimal weight: 5.9990 chunk 190 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 266 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 180 HIS ** 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** I 28 GLN I 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.196672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154285 restraints weight = 30970.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151318 restraints weight = 27462.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154868 restraints weight = 24582.821| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25158 Z= 0.134 Angle : 0.556 11.994 34151 Z= 0.288 Chirality : 0.041 0.248 3720 Planarity : 0.004 0.065 4381 Dihedral : 5.563 57.285 3373 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.65 % Allowed : 20.08 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3040 helix: 1.40 (0.13), residues: 1526 sheet: -1.50 (0.26), residues: 394 loop : -0.62 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 174 HIS 0.021 0.001 HIS B 178 PHE 0.038 0.002 PHE J 115 TYR 0.040 0.002 TYR B 548 ARG 0.009 0.000 ARG J 33 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1169) hydrogen bonds : angle 4.83812 ( 3402) covalent geometry : bond 0.00306 (25158) covalent geometry : angle 0.55602 (34151) *********************** 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 466 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 371 time to evaluate : 2.954 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: 0.7302 (m-80) cc_final: 0.6664 (m-80) REVERT: B 94 MET cc_start: 0.2318 (mmp) cc_final: 0.1923 (mmt) REVERT: B 250 HIS cc_start: 0.6610 (t70) cc_final: 0.6258 (p-80) REVERT: B 351 TYR cc_start: 0.6675 (t80) cc_final: 0.6465 (m-80) REVERT: B 528 SER cc_start: 0.7192 (OUTLIER) cc_final: 0.6472 (t) REVERT: B 542 ILE cc_start: 0.6201 (mm) cc_final: 0.5008 (pt) REVERT: C 243 CYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6485 (m) REVERT: C 450 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.6998 (p0) REVERT: C 540 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6681 (mm-30) REVERT: C 615 LYS cc_start: 0.8234 (mmtm) cc_final: 0.7927 (ttmt) REVERT: D 57 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7498 (tm-30) REVERT: D 180 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.8006 (m170) REVERT: D 221 TYR cc_start: 0.6523 (m-80) cc_final: 0.6218 (m-80) REVERT: D 236 ARG cc_start: 0.7907 (mmt90) cc_final: 0.7558 (mmt90) REVERT: A 81 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6988 (tm-30) REVERT: A 100 LYS cc_start: 0.7202 (mtmp) cc_final: 0.6475 (mttp) REVERT: A 102 TYR cc_start: 0.7688 (m-10) cc_final: 0.7319 (m-10) REVERT: A 477 PHE cc_start: 0.8000 (t80) cc_final: 0.7783 (t80) REVERT: A 579 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (tpt90) REVERT: I 1 MET cc_start: 0.7036 (mmm) cc_final: 0.6834 (tpt) REVERT: I 30 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7661 (mmt180) REVERT: H 333 MET cc_start: 0.7823 (mtt) cc_final: 0.7592 (pmm) outliers start: 95 outliers final: 70 residues processed: 446 average time/residue: 0.4350 time to fit residues: 317.8623 Evaluate side-chains 410 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 335 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 214 CYS 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 515 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain C residue 24 LEU 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 162 LEU 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 450 ASP Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 115 VAL 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 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 520 THR 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 214 CYS Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 320 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 521 VAL Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 579 ARG 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 E residue 348 TYR Chi-restraints excluded: chain I residue 63 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 235 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 205 optimal weight: 0.0570 chunk 259 optimal weight: 0.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN I 151 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.190600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147792 restraints weight = 31379.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146880 restraints weight = 24554.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148528 restraints weight = 26202.927| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 25158 Z= 0.247 Angle : 0.640 13.328 34151 Z= 0.334 Chirality : 0.045 0.247 3720 Planarity : 0.004 0.070 4381 Dihedral : 5.787 57.045 3372 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.42 % Allowed : 19.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.15), residues: 3040 helix: 1.13 (0.13), residues: 1531 sheet: -1.74 (0.26), residues: 377 loop : -0.79 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 34 HIS 0.007 0.001 HIS D 240 PHE 0.028 0.002 PHE I 137 TYR 0.036 0.002 TYR B 548 ARG 0.013 0.001 ARG G 343 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1169) hydrogen bonds : angle 4.99273 ( 3402) covalent geometry : bond 0.00587 (25158) covalent geometry : angle 0.64025 (34151) *********************** 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 472 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 357 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7313 (m-80) cc_final: 0.6675 (m-80) REVERT: B 351 TYR cc_start: 0.6791 (t80) cc_final: 0.6472 (m-80) REVERT: B 542 ILE cc_start: 0.6252 (mm) cc_final: 0.5030 (pt) REVERT: B 578 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7466 (p) REVERT: C 243 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6524 (m) REVERT: C 315 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8123 (m170) REVERT: C 450 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.6930 (p0) REVERT: C 595 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8106 (tt) REVERT: C 615 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7979 (ttmt) REVERT: D 57 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 100 LYS cc_start: 0.7851 (mttt) cc_final: 0.7433 (tptt) REVERT: D 180 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8020 (m90) REVERT: D 236 ARG cc_start: 0.7904 (mmt90) cc_final: 0.7507 (mmt90) REVERT: D 336 ASN cc_start: 0.8164 (m-40) cc_final: 0.7841 (m-40) REVERT: D 581 GLN cc_start: 0.7780 (mt0) cc_final: 0.7442 (mt0) REVERT: A 52 LYS cc_start: 0.6791 (tmmt) cc_final: 0.6510 (ttmt) REVERT: A 94 MET cc_start: 0.7683 (mmm) cc_final: 0.7397 (ttm) REVERT: A 100 LYS cc_start: 0.7252 (mtmp) cc_final: 0.6332 (mttp) REVERT: A 419 MET cc_start: 0.6971 (tpt) cc_final: 0.6649 (tpt) REVERT: A 579 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7801 (tpt90) REVERT: I 1 MET cc_start: 0.7062 (mmm) cc_final: 0.6845 (tpt) REVERT: I 30 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7712 (mmt180) REVERT: H 333 MET cc_start: 0.7700 (mtt) cc_final: 0.7486 (pmm) outliers start: 115 outliers final: 86 residues processed: 453 average time/residue: 0.5649 time to fit residues: 419.4330 Evaluate side-chains 425 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 332 time to evaluate : 3.068 ------------------------------------------------------------------------------- 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 108 LEU 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 117 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 515 THR Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 578 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 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 315 HIS Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 350 ASN 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 482 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 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 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 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 207 THR Chi-restraints excluded: chain A residue 214 CYS 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 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 548 TYR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 579 ARG 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 E residue 337 SER Chi-restraints excluded: chain I residue 63 VAL 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 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 109 optimal weight: 0.4980 chunk 293 optimal weight: 0.9990 chunk 290 optimal weight: 0.9980 chunk 270 optimal weight: 0.8980 chunk 245 optimal weight: 0.4980 chunk 210 optimal weight: 0.6980 chunk 273 optimal weight: 0.3980 chunk 288 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** B 541 HIS C 149 ASN D 180 HIS D 222 ASN ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.195336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.153351 restraints weight = 31035.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152920 restraints weight = 23821.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154202 restraints weight = 25596.958| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25158 Z= 0.126 Angle : 0.558 11.647 34151 Z= 0.290 Chirality : 0.041 0.253 3720 Planarity : 0.004 0.072 4381 Dihedral : 5.575 58.953 3370 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.35 % Allowed : 20.54 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3040 helix: 1.30 (0.13), residues: 1534 sheet: -1.65 (0.26), residues: 389 loop : -0.65 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 174 HIS 0.005 0.001 HIS D 180 PHE 0.029 0.002 PHE C 220 TYR 0.033 0.002 TYR C 68 ARG 0.007 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1169) hydrogen bonds : angle 4.79871 ( 3402) covalent geometry : bond 0.00286 (25158) covalent geometry : angle 0.55775 (34151) *********************** 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 438 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 351 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7212 (m-80) cc_final: 0.6575 (m-80) REVERT: B 94 MET cc_start: 0.2703 (mmp) cc_final: 0.1268 (mmm) REVERT: B 351 TYR cc_start: 0.6699 (t80) cc_final: 0.6482 (m-80) REVERT: B 463 ILE cc_start: 0.8126 (tp) cc_final: 0.7882 (tp) REVERT: B 542 ILE cc_start: 0.6130 (mm) cc_final: 0.4900 (pt) REVERT: B 578 SER cc_start: 0.7697 (OUTLIER) cc_final: 0.7468 (p) REVERT: C 30 PHE cc_start: 0.8172 (m-80) cc_final: 0.7819 (m-80) REVERT: C 242 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7671 (t80) REVERT: C 450 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6768 (p0) REVERT: C 615 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7977 (ttmt) REVERT: D 57 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: D 100 LYS cc_start: 0.7860 (mttt) cc_final: 0.7452 (mmtt) REVERT: D 221 TYR cc_start: 0.6562 (m-80) cc_final: 0.6243 (m-80) REVERT: D 236 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7498 (mmt90) REVERT: D 304 ILE cc_start: 0.8414 (mm) cc_final: 0.8201 (mt) REVERT: D 581 GLN cc_start: 0.7675 (mt0) cc_final: 0.7360 (mt0) REVERT: A 52 LYS cc_start: 0.6779 (tmmt) cc_final: 0.6428 (ttmt) REVERT: A 100 LYS cc_start: 0.7105 (mtmp) cc_final: 0.6443 (mttp) REVERT: E 342 LYS cc_start: 0.8465 (ttpt) cc_final: 0.8253 (ttpp) REVERT: I 30 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7695 (mmt180) REVERT: H 344 LYS cc_start: 0.8258 (tptt) cc_final: 0.7785 (tptm) outliers start: 87 outliers final: 68 residues processed: 424 average time/residue: 0.5422 time to fit residues: 368.9142 Evaluate side-chains 394 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 322 time to evaluate : 8.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 LEU 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 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 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 578 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 242 TYR 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 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 57 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 VAL 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 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 124 TRP 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 568 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 160 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN C 149 ASN D 174 HIS ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.184157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140609 restraints weight = 31626.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140584 restraints weight = 25340.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.141744 restraints weight = 25116.726| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25158 Z= 0.269 Angle : 0.663 13.259 34151 Z= 0.347 Chirality : 0.046 0.258 3720 Planarity : 0.005 0.076 4381 Dihedral : 5.822 59.670 3370 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.62 % Allowed : 20.50 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3040 helix: 1.04 (0.13), residues: 1527 sheet: -1.91 (0.27), residues: 366 loop : -0.86 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J 174 HIS 0.007 0.001 HIS D 240 PHE 0.030 0.002 PHE I 137 TYR 0.036 0.002 TYR C 239 ARG 0.014 0.001 ARG G 343 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 1169) hydrogen bonds : angle 5.00300 ( 3402) covalent geometry : bond 0.00636 (25158) covalent geometry : angle 0.66281 (34151) *********************** 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 433 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 339 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7325 (m-80) cc_final: 0.6560 (m-80) REVERT: B 351 TYR cc_start: 0.6916 (t80) cc_final: 0.6422 (m-80) REVERT: B 463 ILE cc_start: 0.8124 (tp) cc_final: 0.7901 (tp) REVERT: B 538 MET cc_start: 0.5613 (tpt) cc_final: 0.5310 (tpt) REVERT: B 542 ILE cc_start: 0.6074 (mm) cc_final: 0.4867 (pt) REVERT: B 578 SER cc_start: 0.7687 (OUTLIER) cc_final: 0.7465 (p) REVERT: B 611 MET cc_start: 0.4120 (mmt) cc_final: 0.3904 (mmt) REVERT: C 30 PHE cc_start: 0.8266 (m-80) cc_final: 0.7851 (m-80) REVERT: C 88 LYS cc_start: 0.9231 (tptp) cc_final: 0.8651 (ttmm) REVERT: C 227 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: C 315 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.8174 (m170) REVERT: C 450 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.6906 (p0) REVERT: C 615 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7948 (ttmt) REVERT: D 100 LYS cc_start: 0.7863 (mttt) cc_final: 0.7329 (tptt) REVERT: D 180 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.7730 (m90) REVERT: D 236 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7516 (mmt90) REVERT: D 581 GLN cc_start: 0.7940 (mt0) cc_final: 0.7723 (mt0) REVERT: A 52 LYS cc_start: 0.6686 (tmmt) cc_final: 0.6335 (ttmt) REVERT: A 100 LYS cc_start: 0.7224 (mtmp) cc_final: 0.6458 (mttp) REVERT: E 342 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8355 (ttmm) REVERT: I 30 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7594 (mmt180) REVERT: H 344 LYS cc_start: 0.8195 (tptt) cc_final: 0.7707 (tptm) outliers start: 94 outliers final: 78 residues processed: 422 average time/residue: 0.3622 time to fit residues: 242.9697 Evaluate side-chains 406 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 51 LEU 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 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 129 TRP 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 578 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 143 TRP Chi-restraints excluded: chain C residue 153 LEU 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 323 THR Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 379 THR 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 528 SER Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 115 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 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 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 124 TRP Chi-restraints excluded: chain A residue 158 THR 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 568 THR 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 120 LEU Chi-restraints excluded: chain I residue 121 SER 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 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 195 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 251 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 269 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.189378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145264 restraints weight = 31130.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145039 restraints weight = 22754.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146715 restraints weight = 23203.508| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25158 Z= 0.136 Angle : 0.580 12.305 34151 Z= 0.300 Chirality : 0.042 0.266 3720 Planarity : 0.004 0.076 4381 Dihedral : 5.632 59.677 3370 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.88 % Allowed : 21.46 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 3040 helix: 1.26 (0.13), residues: 1528 sheet: -1.77 (0.26), residues: 388 loop : -0.69 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP J 174 HIS 0.005 0.001 HIS C 240 PHE 0.024 0.002 PHE D 103 TYR 0.038 0.002 TYR A 509 ARG 0.007 0.000 ARG C 211 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 1169) hydrogen bonds : angle 4.81567 ( 3402) covalent geometry : bond 0.00315 (25158) covalent geometry : angle 0.57958 (34151) ********************** 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 417 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 342 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 95 TYR cc_start: 0.7252 (m-80) cc_final: 0.6464 (m-80) REVERT: B 351 TYR cc_start: 0.6901 (t80) cc_final: 0.6351 (m-80) REVERT: B 492 ASP cc_start: 0.6817 (t0) cc_final: 0.6034 (p0) REVERT: B 538 MET cc_start: 0.5376 (tpt) cc_final: 0.5146 (tpt) REVERT: B 542 ILE cc_start: 0.5868 (mm) cc_final: 0.4710 (pt) REVERT: B 578 SER cc_start: 0.7627 (OUTLIER) cc_final: 0.7411 (p) REVERT: C 88 LYS cc_start: 0.9207 (tptp) cc_final: 0.8635 (ttmm) REVERT: C 227 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: C 242 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7661 (t80) REVERT: C 315 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8010 (m170) REVERT: C 450 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.6751 (p0) REVERT: C 615 LYS cc_start: 0.8292 (mmtm) cc_final: 0.7879 (ttmt) REVERT: D 221 TYR cc_start: 0.6585 (m-80) cc_final: 0.6360 (m-80) REVERT: D 236 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7460 (mmt90) REVERT: D 304 ILE cc_start: 0.8421 (mm) cc_final: 0.8196 (mt) REVERT: D 581 GLN cc_start: 0.7768 (mt0) cc_final: 0.7546 (mt0) REVERT: A 52 LYS cc_start: 0.6658 (tmmt) cc_final: 0.6323 (ttmt) REVERT: A 100 LYS cc_start: 0.6948 (mtmp) cc_final: 0.6355 (mttp) REVERT: I 30 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.7564 (mmt180) REVERT: H 344 LYS cc_start: 0.8147 (tptt) cc_final: 0.7668 (tptm) outliers start: 75 outliers final: 61 residues processed: 410 average time/residue: 0.3730 time to fit residues: 244.2652 Evaluate side-chains 395 residues out of total 2665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 329 time to evaluate : 2.765 ------------------------------------------------------------------------------- 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 115 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 316 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 578 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 153 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 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 350 ASN Chi-restraints excluded: chain C residue 379 THR 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 79 LEU Chi-restraints excluded: chain D residue 115 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 389 LEU Chi-restraints excluded: chain D residue 457 LEU 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 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 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 I residue 63 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 145 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 266 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 191 optimal weight: 0.9980 chunk 240 optimal weight: 0.0980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.190072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.145922 restraints weight = 31099.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146451 restraints weight = 22802.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148064 restraints weight = 22478.922| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25158 Z= 0.135 Angle : 0.573 11.107 34151 Z= 0.296 Chirality : 0.041 0.253 3720 Planarity : 0.004 0.079 4381 Dihedral : 5.468 59.365 3369 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.65 % Allowed : 21.88 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3040 helix: 1.34 (0.13), residues: 1525 sheet: -1.77 (0.26), residues: 386 loop : -0.63 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 34 HIS 0.004 0.001 HIS C 240 PHE 0.022 0.002 PHE D 103 TYR 0.032 0.002 TYR A 509 ARG 0.020 0.000 ARG G 343 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 1169) hydrogen bonds : angle 4.73878 ( 3402) covalent geometry : bond 0.00314 (25158) covalent geometry : angle 0.57309 (34151) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9320.96 seconds wall clock time: 170 minutes 50.11 seconds (10250.11 seconds total)