Starting phenix.real_space_refine on Tue Jun 17 01:00:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6p_25723/06_2025/7t6p_25723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6p_25723/06_2025/7t6p_25723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6p_25723/06_2025/7t6p_25723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6p_25723/06_2025/7t6p_25723.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6p_25723/06_2025/7t6p_25723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6p_25723/06_2025/7t6p_25723.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.055 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 10.66, per 1000 atoms: 0.55 Number of scatterers: 19412 At special positions: 0 Unit cell: (143.1, 143.1, 121.9, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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: 4.26 Conformation dependent library (CDL) restraints added in 2.3 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 8 sheets defined 65.3% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.740A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.882A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.940A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.655A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.653A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.096A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.769A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.917A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.816A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 306 through 309 removed outlier: 3.577A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.108A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 380 through 410 Proline residue: A 405 - end of helix removed outlier: 3.826A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 4.388A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.660A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 510 removed outlier: 4.161A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.575A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.566A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 604 removed outlier: 3.833A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.780A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.881A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 106 removed outlier: 3.958A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.642A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.573A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 4.082A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 4.031A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.719A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.556A pdb=" N LEU B 234 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 235' Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.825A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 306 through 309 removed outlier: 3.571A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 310 through 324 removed outlier: 4.113A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 380 through 410 Proline residue: B 405 - end of helix removed outlier: 3.815A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 4.378A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.664A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 510 removed outlier: 4.132A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.624A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.528A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 604 removed outlier: 3.828A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.706A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.932A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.587A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.531A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.853A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 4.105A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 removed outlier: 3.601A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.531A pdb=" N LEU C 234 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.001A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 306 through 309 removed outlier: 3.514A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.204A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.682A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.828A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 4.558A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.648A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 510 removed outlier: 4.028A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.626A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 Processing helix chain 'C' and resid 569 through 604 removed outlier: 4.075A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN C 587 " --> pdb=" O TRP C 583 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.742A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.879A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 106 removed outlier: 3.940A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.655A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.583A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 4.098A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 4.038A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 3.729A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.550A pdb=" N LEU D 234 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 235' Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.838A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 306 through 309 Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.085A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 380 through 410 Proline residue: D 405 - end of helix removed outlier: 3.803A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 4.378A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.664A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 510 removed outlier: 4.174A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.633A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.551A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 604 removed outlier: 3.849A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.837A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.852A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.809A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.851A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1060 hydrogen bonds defined for protein. 3135 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: 5.53 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6103 1.34 - 1.46: 3961 1.46 - 1.58: 9568 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.26e+01 bond pdb=" C THR A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.337 1.381 -0.044 1.24e-02 6.50e+03 1.25e+01 bond pdb=" CG1 ILE D 501 " pdb=" CD1 ILE D 501 " ideal model delta sigma weight residual 1.513 1.381 0.132 3.90e-02 6.57e+02 1.14e+01 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.24e-02 6.50e+03 1.13e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 25898 2.49 - 4.97: 819 4.97 - 7.46: 174 7.46 - 9.95: 57 9.95 - 12.44: 16 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C LEU D 604 " pdb=" N GLU D 605 " pdb=" CA GLU D 605 " ideal model delta sigma weight residual 121.54 133.71 -12.17 1.91e+00 2.74e-01 4.06e+01 angle pdb=" C LEU A 604 " pdb=" N GLU A 605 " pdb=" CA GLU A 605 " ideal model delta sigma weight residual 121.54 133.68 -12.14 1.91e+00 2.74e-01 4.04e+01 angle pdb=" C LEU B 604 " pdb=" N GLU B 605 " pdb=" CA GLU B 605 " ideal model delta sigma weight residual 121.54 133.64 -12.10 1.91e+00 2.74e-01 4.01e+01 angle pdb=" C VAL C 378 " pdb=" N THR C 379 " pdb=" CA THR C 379 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C PRO B 362 " pdb=" N ARG B 363 " pdb=" CA ARG B 363 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 10391 15.92 - 31.84: 1060 31.84 - 47.75: 274 47.75 - 63.67: 59 63.67 - 79.59: 28 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE A 510 " pdb=" C ILE A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 146.06 33.94 0 5.00e+00 4.00e-02 4.61e+01 dihedral pdb=" CA ILE C 510 " pdb=" C ILE C 510 " pdb=" N THR C 511 " pdb=" CA THR C 511 " ideal model delta harmonic sigma weight residual 180.00 146.44 33.56 0 5.00e+00 4.00e-02 4.50e+01 dihedral pdb=" CA THR D 514 " pdb=" C THR D 514 " pdb=" N GLU D 515 " pdb=" CA GLU D 515 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2699 0.088 - 0.175: 327 0.175 - 0.263: 32 0.263 - 0.350: 8 0.350 - 0.438: 6 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB THR C 379 " pdb=" CA THR C 379 " pdb=" OG1 THR C 379 " pdb=" CG2 THR C 379 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CB THR A 379 " pdb=" CA THR A 379 " pdb=" OG1 THR A 379 " pdb=" CG2 THR A 379 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CB THR B 379 " pdb=" CA THR B 379 " pdb=" OG1 THR B 379 " pdb=" CG2 THR B 379 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 511 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C THR D 511 " 0.048 2.00e-02 2.50e+03 pdb=" O THR D 511 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE D 512 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 585 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C VAL D 585 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL D 585 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA D 586 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 511 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C THR B 511 " 0.047 2.00e-02 2.50e+03 pdb=" O THR B 511 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE B 512 " -0.016 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5711 2.83 - 3.35: 17920 3.35 - 3.86: 33109 3.86 - 4.38: 39220 4.38 - 4.90: 65697 Nonbonded interactions: 161657 Sorted by model distance: nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.310 3.040 nonbonded pdb=" O LEU C 568 " pdb=" ND2 ASN C 572 " model vdw 2.368 3.120 nonbonded pdb=" O LEU D 568 " pdb=" ND2 ASN D 572 " model vdw 2.377 3.120 nonbonded pdb=" OE1 GLN A 73 " pdb=" NH1 ARG A 75 " model vdw 2.379 3.120 nonbonded pdb=" O LEU B 218 " pdb=" OG SER B 221 " model vdw 2.379 3.040 ... (remaining 161652 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.030 Extract box with map and model: 0.700 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 40.380 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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 : 0.005 0.132 19860 Z= 0.273 Angle : 1.127 12.437 26964 Z= 0.596 Chirality : 0.061 0.438 3072 Planarity : 0.008 0.067 3416 Dihedral : 14.543 79.591 7236 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.37 (0.13), residues: 2408 helix: -2.24 (0.10), residues: 1444 sheet: -1.71 (0.51), residues: 64 loop : -1.97 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 583 HIS 0.008 0.001 HIS A 637 PHE 0.029 0.003 PHE C 456 TYR 0.039 0.002 TYR A 328 ARG 0.005 0.001 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.15518 ( 1060) hydrogen bonds : angle 7.10612 ( 3135) covalent geometry : bond 0.00531 (19860) covalent geometry : angle 1.12704 (26964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 2.009 Fit side-chains revert: symmetry clash REVERT: A 51 GLN cc_start: 0.7699 (tp-100) cc_final: 0.7494 (tp-100) REVERT: A 55 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 257 GLN cc_start: 0.7004 (mm110) cc_final: 0.6578 (tp40) REVERT: A 497 MET cc_start: 0.7923 (ttt) cc_final: 0.7676 (ttt) REVERT: A 515 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6113 (mm-30) REVERT: A 583 TRP cc_start: 0.8131 (p-90) cc_final: 0.7877 (p-90) REVERT: B 51 GLN cc_start: 0.7682 (tp-100) cc_final: 0.7467 (tp-100) REVERT: B 55 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 257 GLN cc_start: 0.7030 (mm110) cc_final: 0.6720 (mm110) REVERT: B 429 ILE cc_start: 0.7628 (mt) cc_final: 0.7377 (tp) REVERT: B 447 MET cc_start: 0.7461 (mtm) cc_final: 0.7190 (ptm) REVERT: C 51 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7482 (tp-100) REVERT: C 55 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 181 LEU cc_start: 0.8399 (tt) cc_final: 0.8170 (tm) REVERT: C 239 GLN cc_start: 0.8047 (tt0) cc_final: 0.7828 (tt0) REVERT: D 257 GLN cc_start: 0.7158 (mm110) cc_final: 0.6939 (mm110) REVERT: D 260 MET cc_start: 0.7342 (mmp) cc_final: 0.7080 (mmt) REVERT: D 447 MET cc_start: 0.7485 (mtm) cc_final: 0.7242 (ptm) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 1.2077 time to fit residues: 568.0184 Evaluate side-chains 316 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 374 GLN A 380 HIS B 185 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN B 380 HIS C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 185 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN D 380 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.154627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117976 restraints weight = 23837.422| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.35 r_work: 0.3301 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 19860 Z= 0.175 Angle : 0.659 10.008 26964 Z= 0.340 Chirality : 0.044 0.248 3072 Planarity : 0.005 0.046 3416 Dihedral : 5.004 25.000 2644 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.58 % Allowed : 11.12 % Favored : 86.31 % 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: -1.46 (0.15), residues: 2408 helix: -0.37 (0.12), residues: 1480 sheet: -2.02 (0.48), residues: 84 loop : -1.77 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 629 HIS 0.005 0.001 HIS C 84 PHE 0.021 0.001 PHE A 611 TYR 0.019 0.002 TYR B 555 ARG 0.005 0.001 ARG B 305 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 1060) hydrogen bonds : angle 4.51082 ( 3135) covalent geometry : bond 0.00409 (19860) covalent geometry : angle 0.65868 (26964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 357 time to evaluate : 2.044 Fit side-chains REVERT: A 51 GLN cc_start: 0.7505 (tp-100) cc_final: 0.7299 (tp-100) REVERT: A 55 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 214 GLN cc_start: 0.7496 (mp10) cc_final: 0.6894 (mp10) REVERT: A 294 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7242 (mt-10) REVERT: A 315 GLU cc_start: 0.8004 (mp0) cc_final: 0.7548 (mp0) REVERT: A 380 HIS cc_start: 0.7008 (t-170) cc_final: 0.6788 (t70) REVERT: A 381 GLN cc_start: 0.6942 (mp10) cc_final: 0.5962 (mt0) REVERT: A 487 PHE cc_start: 0.7551 (m-10) cc_final: 0.7331 (m-10) REVERT: A 497 MET cc_start: 0.7593 (ttt) cc_final: 0.7311 (ttt) REVERT: B 214 GLN cc_start: 0.7407 (mp10) cc_final: 0.6922 (mp10) REVERT: B 315 GLU cc_start: 0.8052 (mp0) cc_final: 0.7616 (mp0) REVERT: B 349 TYR cc_start: 0.8236 (m-80) cc_final: 0.7987 (m-80) REVERT: B 380 HIS cc_start: 0.6980 (t-170) cc_final: 0.6756 (t70) REVERT: B 381 GLN cc_start: 0.6920 (mp10) cc_final: 0.5935 (mt0) REVERT: B 487 PHE cc_start: 0.7575 (m-10) cc_final: 0.7332 (m-10) REVERT: C 55 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 62 LYS cc_start: 0.7815 (mtmm) cc_final: 0.7541 (mttt) REVERT: C 214 GLN cc_start: 0.7497 (mp10) cc_final: 0.6877 (mp10) REVERT: C 215 MET cc_start: 0.8420 (mmm) cc_final: 0.8162 (tpp) REVERT: C 222 TYR cc_start: 0.7035 (m-80) cc_final: 0.6660 (m-80) REVERT: C 257 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6667 (mm110) REVERT: C 315 GLU cc_start: 0.7898 (mp0) cc_final: 0.7272 (mp0) REVERT: C 497 MET cc_start: 0.7538 (ttt) cc_final: 0.7170 (ttt) REVERT: D 55 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7722 (mt-10) REVERT: D 214 GLN cc_start: 0.7396 (mp10) cc_final: 0.6916 (mp10) REVERT: D 315 GLU cc_start: 0.7948 (mp0) cc_final: 0.7516 (mp0) REVERT: D 380 HIS cc_start: 0.7018 (t-170) cc_final: 0.6800 (t70) REVERT: D 381 GLN cc_start: 0.6929 (mp10) cc_final: 0.5943 (mt0) REVERT: D 487 PHE cc_start: 0.7581 (m-10) cc_final: 0.7380 (m-10) outliers start: 54 outliers final: 9 residues processed: 378 average time/residue: 1.1759 time to fit residues: 506.0342 Evaluate side-chains 303 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 294 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 382 ASP Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 372 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 310 GLN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 310 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 374 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 310 GLN D 369 GLN D 374 GLN D 635 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110745 restraints weight = 23197.696| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.37 r_work: 0.3165 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19860 Z= 0.189 Angle : 0.630 6.624 26964 Z= 0.326 Chirality : 0.043 0.210 3072 Planarity : 0.005 0.049 3416 Dihedral : 4.873 26.770 2644 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.67 % Allowed : 14.79 % Favored : 82.54 % 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: -0.70 (0.16), residues: 2408 helix: 0.34 (0.13), residues: 1484 sheet: -1.93 (0.43), residues: 104 loop : -1.67 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 583 HIS 0.005 0.001 HIS B 122 PHE 0.013 0.001 PHE D 523 TYR 0.013 0.002 TYR C 555 ARG 0.005 0.001 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 1060) hydrogen bonds : angle 4.34338 ( 3135) covalent geometry : bond 0.00451 (19860) covalent geometry : angle 0.62987 (26964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 305 time to evaluate : 2.153 Fit side-chains REVERT: A 55 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 99 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.5298 (mpp) REVERT: A 214 GLN cc_start: 0.7588 (mp10) cc_final: 0.6877 (mp10) REVERT: A 294 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7263 (mt-10) REVERT: A 315 GLU cc_start: 0.7974 (mp0) cc_final: 0.7337 (mp0) REVERT: A 349 TYR cc_start: 0.8118 (m-80) cc_final: 0.7805 (m-80) REVERT: A 381 GLN cc_start: 0.6924 (mp10) cc_final: 0.6018 (mt0) REVERT: A 429 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6823 (tp) REVERT: A 497 MET cc_start: 0.7412 (ttt) cc_final: 0.7142 (ttt) REVERT: B 55 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 214 GLN cc_start: 0.7391 (mp10) cc_final: 0.6794 (mp10) REVERT: B 257 GLN cc_start: 0.6658 (mm-40) cc_final: 0.6455 (tp40) REVERT: B 315 GLU cc_start: 0.8016 (mp0) cc_final: 0.7383 (mp0) REVERT: B 349 TYR cc_start: 0.8140 (m-80) cc_final: 0.7828 (m-80) REVERT: B 381 GLN cc_start: 0.6920 (mp10) cc_final: 0.6015 (mt0) REVERT: C 55 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7503 (mt-10) REVERT: C 62 LYS cc_start: 0.7856 (mtmm) cc_final: 0.7505 (mttt) REVERT: C 97 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6938 (mp) REVERT: C 214 GLN cc_start: 0.7593 (mp10) cc_final: 0.6908 (mp10) REVERT: C 215 MET cc_start: 0.8420 (mmm) cc_final: 0.8085 (tpp) REVERT: C 315 GLU cc_start: 0.7906 (mp0) cc_final: 0.7204 (mp0) REVERT: C 497 MET cc_start: 0.7518 (ttt) cc_final: 0.7218 (ttt) REVERT: D 55 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7544 (mt-10) REVERT: D 99 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.5564 (mpp) REVERT: D 214 GLN cc_start: 0.7399 (mp10) cc_final: 0.6813 (mp10) REVERT: D 315 GLU cc_start: 0.7978 (mp0) cc_final: 0.7302 (mp0) REVERT: D 318 SER cc_start: 0.7886 (m) cc_final: 0.7598 (t) REVERT: D 349 TYR cc_start: 0.8116 (m-80) cc_final: 0.7833 (m-80) REVERT: D 381 GLN cc_start: 0.6931 (mp10) cc_final: 0.6030 (mt0) REVERT: D 515 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6948 (mp0) outliers start: 56 outliers final: 15 residues processed: 332 average time/residue: 1.2450 time to fit residues: 467.9941 Evaluate side-chains 289 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 269 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 515 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 310 GLN A 374 GLN A 635 ASN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 369 GLN B 374 GLN B 635 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 310 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN D 261 GLN D 310 GLN D 374 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108826 restraints weight = 23367.420| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.34 r_work: 0.3141 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19860 Z= 0.190 Angle : 0.638 10.546 26964 Z= 0.325 Chirality : 0.044 0.311 3072 Planarity : 0.005 0.048 3416 Dihedral : 4.783 26.623 2644 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.96 % Allowed : 17.75 % Favored : 79.29 % 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: -0.29 (0.17), residues: 2408 helix: 0.70 (0.13), residues: 1484 sheet: -1.92 (0.43), residues: 104 loop : -1.54 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 583 HIS 0.003 0.001 HIS B 122 PHE 0.014 0.001 PHE D 611 TYR 0.014 0.002 TYR D 555 ARG 0.004 0.000 ARG D 43 Details of bonding type rmsd hydrogen bonds : bond 0.04286 ( 1060) hydrogen bonds : angle 4.28962 ( 3135) covalent geometry : bond 0.00455 (19860) covalent geometry : angle 0.63761 (26964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 286 time to evaluate : 2.329 Fit side-chains REVERT: A 214 GLN cc_start: 0.7610 (mp10) cc_final: 0.6923 (mp10) REVERT: A 234 LEU cc_start: 0.8064 (mp) cc_final: 0.7786 (mm) REVERT: A 294 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7402 (mt-10) REVERT: A 315 GLU cc_start: 0.7951 (mp0) cc_final: 0.7222 (mp0) REVERT: A 318 SER cc_start: 0.7829 (m) cc_final: 0.7605 (t) REVERT: A 349 TYR cc_start: 0.8106 (m-80) cc_final: 0.7771 (m-80) REVERT: A 381 GLN cc_start: 0.6954 (mp10) cc_final: 0.6090 (mt0) REVERT: A 429 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6827 (tp) REVERT: A 497 MET cc_start: 0.7330 (ttt) cc_final: 0.7092 (ttt) REVERT: B 214 GLN cc_start: 0.7526 (mp10) cc_final: 0.6901 (mp10) REVERT: B 257 GLN cc_start: 0.6628 (mm-40) cc_final: 0.6401 (tp40) REVERT: B 315 GLU cc_start: 0.7980 (mp0) cc_final: 0.7271 (mp0) REVERT: B 318 SER cc_start: 0.7821 (m) cc_final: 0.7579 (t) REVERT: B 349 TYR cc_start: 0.8134 (m-80) cc_final: 0.7806 (m-80) REVERT: B 381 GLN cc_start: 0.6926 (mp10) cc_final: 0.6063 (mt0) REVERT: B 528 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.6944 (p) REVERT: C 62 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7571 (mttt) REVERT: C 214 GLN cc_start: 0.7628 (mp10) cc_final: 0.6975 (mp10) REVERT: C 294 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7153 (mt-10) REVERT: C 315 GLU cc_start: 0.7917 (mp0) cc_final: 0.7129 (mp0) REVERT: C 318 SER cc_start: 0.7852 (m) cc_final: 0.7603 (t) REVERT: C 429 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6686 (tp) REVERT: C 497 MET cc_start: 0.7449 (ttt) cc_final: 0.7179 (ttt) REVERT: D 99 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.5537 (mpp) REVERT: D 214 GLN cc_start: 0.7549 (mp10) cc_final: 0.6922 (mp10) REVERT: D 257 GLN cc_start: 0.6839 (mm-40) cc_final: 0.6535 (mm110) REVERT: D 315 GLU cc_start: 0.7951 (mp0) cc_final: 0.7296 (mp0) REVERT: D 318 SER cc_start: 0.7835 (m) cc_final: 0.7582 (t) REVERT: D 349 TYR cc_start: 0.8122 (m-80) cc_final: 0.7820 (m-80) REVERT: D 381 GLN cc_start: 0.6939 (mp10) cc_final: 0.6079 (mt0) REVERT: D 429 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6680 (tp) REVERT: D 515 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: D 528 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7018 (p) outliers start: 62 outliers final: 25 residues processed: 319 average time/residue: 1.2841 time to fit residues: 462.6692 Evaluate side-chains 299 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 233 optimal weight: 0.3980 chunk 207 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN A 261 GLN A 310 GLN A 374 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 374 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN C 128 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 310 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 374 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.147323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109473 restraints weight = 23347.305| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.35 r_work: 0.3152 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19860 Z= 0.164 Angle : 0.606 7.535 26964 Z= 0.309 Chirality : 0.042 0.280 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.692 27.122 2644 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.91 % Allowed : 17.75 % Favored : 78.34 % 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: 0.02 (0.17), residues: 2408 helix: 0.91 (0.14), residues: 1492 sheet: -1.91 (0.44), residues: 104 loop : -1.36 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 583 HIS 0.004 0.001 HIS A 637 PHE 0.013 0.001 PHE D 611 TYR 0.014 0.001 TYR D 555 ARG 0.009 0.000 ARG A 414 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 1060) hydrogen bonds : angle 4.17674 ( 3135) covalent geometry : bond 0.00390 (19860) covalent geometry : angle 0.60632 (26964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 281 time to evaluate : 2.052 Fit side-chains REVERT: A 99 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.5541 (mpp) REVERT: A 214 GLN cc_start: 0.7628 (mp10) cc_final: 0.6938 (mp10) REVERT: A 234 LEU cc_start: 0.8041 (mp) cc_final: 0.7780 (mm) REVERT: A 294 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 315 GLU cc_start: 0.7935 (mp0) cc_final: 0.7280 (mp0) REVERT: A 318 SER cc_start: 0.7880 (m) cc_final: 0.7660 (t) REVERT: A 349 TYR cc_start: 0.8109 (m-80) cc_final: 0.7759 (m-80) REVERT: A 429 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6829 (tp) REVERT: A 497 MET cc_start: 0.7284 (ttt) cc_final: 0.7077 (ttt) REVERT: A 520 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7284 (mp) REVERT: B 55 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 214 GLN cc_start: 0.7581 (mp10) cc_final: 0.6914 (mp10) REVERT: B 294 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7252 (mt-10) REVERT: B 315 GLU cc_start: 0.7977 (mp0) cc_final: 0.7323 (mp0) REVERT: B 318 SER cc_start: 0.7878 (m) cc_final: 0.7639 (t) REVERT: B 349 TYR cc_start: 0.8130 (m-80) cc_final: 0.7761 (m-80) REVERT: B 520 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7313 (mp) REVERT: B 528 THR cc_start: 0.7554 (OUTLIER) cc_final: 0.6970 (p) REVERT: C 62 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7652 (mttt) REVERT: C 214 GLN cc_start: 0.7674 (mp10) cc_final: 0.7323 (mp10) REVERT: C 294 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7349 (mt-10) REVERT: C 315 GLU cc_start: 0.7786 (mp0) cc_final: 0.7016 (mp0) REVERT: C 318 SER cc_start: 0.7847 (m) cc_final: 0.7587 (t) REVERT: C 497 MET cc_start: 0.7368 (ttt) cc_final: 0.7127 (ttt) REVERT: C 501 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 520 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7341 (mp) REVERT: D 55 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7680 (mt-10) REVERT: D 99 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.5445 (mpp) REVERT: D 214 GLN cc_start: 0.7577 (mp10) cc_final: 0.6904 (mp10) REVERT: D 294 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7213 (mt-10) REVERT: D 315 GLU cc_start: 0.7936 (mp0) cc_final: 0.7267 (mp0) REVERT: D 318 SER cc_start: 0.7823 (m) cc_final: 0.7571 (t) REVERT: D 349 TYR cc_start: 0.8112 (m-80) cc_final: 0.7752 (m-80) REVERT: D 429 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6662 (tp) REVERT: D 515 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7368 (mm-30) REVERT: D 528 THR cc_start: 0.7588 (OUTLIER) cc_final: 0.6999 (p) outliers start: 82 outliers final: 27 residues processed: 339 average time/residue: 1.2631 time to fit residues: 488.8582 Evaluate side-chains 302 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 310 GLN A 374 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 369 GLN B 374 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 310 GLN D 374 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110758 restraints weight = 23397.140| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.37 r_work: 0.3158 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19860 Z= 0.146 Angle : 0.601 9.833 26964 Z= 0.302 Chirality : 0.041 0.234 3072 Planarity : 0.004 0.048 3416 Dihedral : 4.616 27.419 2644 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.39 % Allowed : 18.94 % Favored : 77.67 % 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 (0.17), residues: 2408 helix: 1.07 (0.14), residues: 1488 sheet: -1.90 (0.44), residues: 104 loop : -1.15 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 286 HIS 0.003 0.001 HIS C 84 PHE 0.012 0.001 PHE D 611 TYR 0.013 0.001 TYR D 555 ARG 0.007 0.000 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1060) hydrogen bonds : angle 4.12210 ( 3135) covalent geometry : bond 0.00340 (19860) covalent geometry : angle 0.60075 (26964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 292 time to evaluate : 2.168 Fit side-chains REVERT: A 75 ARG cc_start: 0.7925 (mmp80) cc_final: 0.7505 (mmp80) REVERT: A 99 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.5342 (mpp) REVERT: A 176 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: A 214 GLN cc_start: 0.7590 (mp10) cc_final: 0.7272 (mp10) REVERT: A 234 LEU cc_start: 0.8010 (mp) cc_final: 0.7759 (mm) REVERT: A 294 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 315 GLU cc_start: 0.7885 (mp0) cc_final: 0.7290 (mp0) REVERT: A 318 SER cc_start: 0.7831 (m) cc_final: 0.7610 (t) REVERT: A 349 TYR cc_start: 0.8024 (m-80) cc_final: 0.7677 (m-80) REVERT: A 379 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7781 (p) REVERT: A 429 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6757 (tp) REVERT: A 497 MET cc_start: 0.7060 (ttt) cc_final: 0.6843 (ttt) REVERT: A 501 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 520 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7205 (mp) REVERT: B 75 ARG cc_start: 0.7946 (mmp80) cc_final: 0.7531 (mmp80) REVERT: B 214 GLN cc_start: 0.7550 (mp10) cc_final: 0.7266 (mp10) REVERT: B 294 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7302 (mt-10) REVERT: B 315 GLU cc_start: 0.7937 (mp0) cc_final: 0.7276 (mp0) REVERT: B 318 SER cc_start: 0.7827 (m) cc_final: 0.7582 (t) REVERT: B 349 TYR cc_start: 0.8056 (m-80) cc_final: 0.7742 (m-80) REVERT: B 381 GLN cc_start: 0.6655 (mp10) cc_final: 0.5877 (mt0) REVERT: B 520 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 528 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.6934 (p) REVERT: C 55 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7459 (mt-10) REVERT: C 62 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7673 (mttt) REVERT: C 214 GLN cc_start: 0.7580 (mp10) cc_final: 0.7200 (mp10) REVERT: C 294 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7369 (mt-10) REVERT: C 315 GLU cc_start: 0.7754 (mp0) cc_final: 0.7187 (mp0) REVERT: C 318 SER cc_start: 0.7801 (m) cc_final: 0.7534 (t) REVERT: C 429 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6617 (tp) REVERT: C 497 MET cc_start: 0.7270 (ttt) cc_final: 0.6960 (ttt) REVERT: C 501 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7662 (mp) REVERT: C 520 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7295 (mp) REVERT: D 75 ARG cc_start: 0.8003 (mmp80) cc_final: 0.7567 (mmp80) REVERT: D 99 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.5432 (mpp) REVERT: D 214 GLN cc_start: 0.7548 (mp10) cc_final: 0.7274 (mp10) REVERT: D 294 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7356 (mt-10) REVERT: D 315 GLU cc_start: 0.7898 (mp0) cc_final: 0.7246 (mp0) REVERT: D 318 SER cc_start: 0.7837 (m) cc_final: 0.7580 (t) REVERT: D 349 TYR cc_start: 0.8027 (m-80) cc_final: 0.7675 (m-80) REVERT: D 379 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7786 (p) REVERT: D 429 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6606 (tp) outliers start: 71 outliers final: 27 residues processed: 335 average time/residue: 1.9311 time to fit residues: 733.5606 Evaluate side-chains 320 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 171 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 232 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 161 optimal weight: 0.0970 chunk 91 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 310 GLN A 374 GLN ** B 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN B 261 GLN B 374 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 374 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113860 restraints weight = 23251.625| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.38 r_work: 0.3224 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19860 Z= 0.115 Angle : 0.570 7.193 26964 Z= 0.288 Chirality : 0.040 0.253 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.465 27.426 2644 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.67 % Allowed : 20.04 % Favored : 77.29 % 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: 0.52 (0.18), residues: 2408 helix: 1.27 (0.14), residues: 1492 sheet: -1.89 (0.44), residues: 104 loop : -1.02 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.003 0.001 HIS A 637 PHE 0.012 0.001 PHE D 611 TYR 0.013 0.001 TYR B 555 ARG 0.010 0.000 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1060) hydrogen bonds : angle 4.02646 ( 3135) covalent geometry : bond 0.00255 (19860) covalent geometry : angle 0.56994 (26964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 302 time to evaluate : 2.765 Fit side-chains revert: symmetry clash REVERT: A 99 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.5311 (mpp) REVERT: A 214 GLN cc_start: 0.7637 (mp10) cc_final: 0.7299 (mp10) REVERT: A 234 LEU cc_start: 0.8004 (mp) cc_final: 0.7787 (mm) REVERT: A 257 GLN cc_start: 0.6706 (mm-40) cc_final: 0.6345 (mm110) REVERT: A 294 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 315 GLU cc_start: 0.7834 (mp0) cc_final: 0.7283 (mp0) REVERT: A 318 SER cc_start: 0.7830 (m) cc_final: 0.7582 (t) REVERT: A 349 TYR cc_start: 0.8036 (m-80) cc_final: 0.7656 (m-80) REVERT: A 429 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6751 (tp) REVERT: B 214 GLN cc_start: 0.7543 (mp10) cc_final: 0.7251 (mp10) REVERT: B 294 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 315 GLU cc_start: 0.7892 (mp0) cc_final: 0.7323 (mp0) REVERT: B 318 SER cc_start: 0.7842 (m) cc_final: 0.7558 (t) REVERT: B 349 TYR cc_start: 0.8075 (m-80) cc_final: 0.7710 (m-80) REVERT: B 528 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7004 (p) REVERT: C 55 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7527 (mt-10) REVERT: C 62 LYS cc_start: 0.7945 (mtmm) cc_final: 0.7613 (mttt) REVERT: C 99 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.5540 (mpp) REVERT: C 214 GLN cc_start: 0.7701 (mp10) cc_final: 0.7310 (mp10) REVERT: C 294 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 315 GLU cc_start: 0.7585 (mp0) cc_final: 0.7111 (mp0) REVERT: C 318 SER cc_start: 0.7794 (m) cc_final: 0.7511 (t) REVERT: C 429 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6610 (tp) REVERT: C 497 MET cc_start: 0.7263 (ttt) cc_final: 0.6957 (ttt) REVERT: D 214 GLN cc_start: 0.7537 (mp10) cc_final: 0.7257 (mp10) REVERT: D 294 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7265 (mt-10) REVERT: D 315 GLU cc_start: 0.7891 (mp0) cc_final: 0.7317 (mp0) REVERT: D 318 SER cc_start: 0.7843 (m) cc_final: 0.7560 (t) REVERT: D 349 TYR cc_start: 0.8056 (m-80) cc_final: 0.7698 (m-80) REVERT: D 429 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6602 (tp) outliers start: 56 outliers final: 22 residues processed: 332 average time/residue: 1.5737 time to fit residues: 596.9470 Evaluate side-chains 299 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 CYS Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 80 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 87 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 229 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 chunk 215 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN A 374 GLN A 637 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 637 HIS ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 374 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.154226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.117866 restraints weight = 23624.385| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.35 r_work: 0.3304 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19860 Z= 0.110 Angle : 0.573 8.327 26964 Z= 0.288 Chirality : 0.040 0.251 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.364 27.456 2644 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.58 % Allowed : 20.66 % Favored : 76.77 % 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: 0.67 (0.18), residues: 2408 helix: 1.37 (0.14), residues: 1496 sheet: -1.87 (0.44), residues: 104 loop : -0.93 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.003 0.001 HIS A 637 PHE 0.012 0.001 PHE D 611 TYR 0.013 0.001 TYR B 555 ARG 0.009 0.000 ARG D 414 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1060) hydrogen bonds : angle 3.97113 ( 3135) covalent geometry : bond 0.00241 (19860) covalent geometry : angle 0.57325 (26964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 291 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.6955 (pt0) cc_final: 0.6467 (pp30) REVERT: A 55 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 214 GLN cc_start: 0.7722 (mp10) cc_final: 0.7443 (mp10) REVERT: A 234 LEU cc_start: 0.8079 (mp) cc_final: 0.7857 (mm) REVERT: A 294 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 315 GLU cc_start: 0.7945 (mp0) cc_final: 0.7445 (mp0) REVERT: A 318 SER cc_start: 0.7964 (m) cc_final: 0.7714 (t) REVERT: A 349 TYR cc_start: 0.8221 (m-80) cc_final: 0.7904 (m-80) REVERT: A 429 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6871 (tp) REVERT: B 112 CYS cc_start: 0.6766 (OUTLIER) cc_final: 0.5916 (m) REVERT: B 214 GLN cc_start: 0.7599 (mp10) cc_final: 0.7276 (mp10) REVERT: B 294 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7391 (mt-10) REVERT: B 315 GLU cc_start: 0.7982 (mp0) cc_final: 0.7439 (mp0) REVERT: B 318 SER cc_start: 0.8081 (m) cc_final: 0.7812 (t) REVERT: B 349 TYR cc_start: 0.8190 (m-80) cc_final: 0.7754 (m-80) REVERT: B 528 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7182 (p) REVERT: C 46 ASP cc_start: 0.7947 (m-30) cc_final: 0.7516 (m-30) REVERT: C 55 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7644 (mt-10) REVERT: C 62 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7670 (mttt) REVERT: C 99 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.5304 (mpp) REVERT: C 214 GLN cc_start: 0.7793 (mp10) cc_final: 0.7398 (mp10) REVERT: C 294 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7356 (mt-10) REVERT: C 315 GLU cc_start: 0.7620 (mp0) cc_final: 0.7194 (mp0) REVERT: C 318 SER cc_start: 0.7942 (m) cc_final: 0.7649 (t) REVERT: C 429 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6722 (tp) REVERT: C 497 MET cc_start: 0.7224 (ttt) cc_final: 0.7019 (ttt) REVERT: D 112 CYS cc_start: 0.6836 (OUTLIER) cc_final: 0.5978 (m) REVERT: D 214 GLN cc_start: 0.7595 (mp10) cc_final: 0.7281 (mp10) REVERT: D 257 GLN cc_start: 0.6434 (tp40) cc_final: 0.6043 (mm110) REVERT: D 294 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7278 (mt-10) REVERT: D 315 GLU cc_start: 0.7931 (mp0) cc_final: 0.7390 (mp0) REVERT: D 318 SER cc_start: 0.7986 (m) cc_final: 0.7704 (t) REVERT: D 349 TYR cc_start: 0.8219 (m-80) cc_final: 0.7873 (m-80) REVERT: D 429 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6718 (tp) outliers start: 54 outliers final: 21 residues processed: 320 average time/residue: 1.1807 time to fit residues: 429.4702 Evaluate side-chains 292 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 112 CYS Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.3619 > 50: distance: 50 - 73: 8.946 distance: 59 - 60: 6.227 distance: 59 - 65: 7.186 distance: 60 - 61: 14.797 distance: 60 - 63: 10.451 distance: 61 - 62: 16.114 distance: 61 - 66: 6.545 distance: 63 - 64: 12.856 distance: 64 - 65: 8.603 distance: 66 - 67: 8.260 distance: 67 - 68: 7.146 distance: 67 - 70: 5.461 distance: 68 - 69: 6.607 distance: 68 - 73: 11.023 distance: 69 - 99: 12.874 distance: 70 - 71: 14.513 distance: 70 - 72: 12.324 distance: 73 - 74: 9.080 distance: 74 - 75: 5.888 distance: 74 - 77: 7.037 distance: 75 - 76: 21.565 distance: 75 - 82: 31.950 distance: 76 - 106: 18.056 distance: 77 - 78: 12.362 distance: 78 - 79: 21.686 distance: 79 - 80: 12.752 distance: 80 - 81: 14.790 distance: 82 - 83: 21.790 distance: 83 - 84: 10.681 distance: 83 - 86: 14.232 distance: 84 - 85: 12.100 distance: 84 - 91: 3.294 distance: 85 - 112: 13.800 distance: 86 - 87: 14.768 distance: 87 - 88: 20.888 distance: 88 - 89: 9.969 distance: 88 - 90: 34.444 distance: 91 - 92: 12.009 distance: 92 - 93: 5.649 distance: 92 - 95: 8.188 distance: 93 - 94: 11.992 distance: 93 - 99: 8.322 distance: 94 - 123: 15.659 distance: 95 - 96: 14.220 distance: 96 - 97: 15.880 distance: 96 - 98: 10.109 distance: 99 - 100: 4.429 distance: 100 - 101: 8.175 distance: 100 - 103: 4.589 distance: 101 - 102: 8.056 distance: 101 - 106: 10.675 distance: 102 - 132: 13.700 distance: 103 - 104: 18.095 distance: 103 - 105: 16.415 distance: 106 - 107: 11.192 distance: 107 - 108: 3.816 distance: 107 - 110: 10.663 distance: 108 - 109: 12.725 distance: 108 - 112: 9.774 distance: 109 - 146: 9.641 distance: 110 - 111: 10.671 distance: 112 - 113: 3.180 distance: 113 - 114: 8.000 distance: 113 - 116: 3.998 distance: 114 - 115: 5.458 distance: 115 - 155: 6.819 distance: 116 - 117: 6.231 distance: 117 - 118: 11.717 distance: 117 - 119: 4.203 distance: 118 - 120: 9.999 distance: 119 - 121: 13.373 distance: 120 - 122: 7.826 distance: 121 - 122: 10.089 distance: 123 - 124: 3.681 distance: 124 - 127: 7.158 distance: 125 - 132: 10.068 distance: 126 - 163: 9.272 distance: 127 - 128: 5.064 distance: 129 - 130: 5.942 distance: 130 - 131: 6.455 distance: 132 - 133: 5.775 distance: 133 - 134: 4.479 distance: 133 - 136: 7.947 distance: 134 - 135: 4.287 distance: 136 - 137: 5.217 distance: 137 - 138: 6.833 distance: 138 - 140: 5.845 distance: 139 - 141: 3.075 distance: 140 - 141: 3.628 distance: 141 - 143: 6.234 distance: 142 - 144: 6.570 distance: 143 - 145: 6.743 distance: 144 - 145: 5.361