Starting phenix.real_space_refine on Fri Jul 3 15:02:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.map" model { file = "/net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z37_14472/07_2026/7z37_14472.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 74 5.16 5 C 9007 2.51 5 N 2423 2.21 5 O 2745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14256 Number of models: 1 Model: "" Number of chains: 6 Chain: "AP1" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5158 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 1 Chain: "BP1" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5173 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 17, 'TRANS': 620} Chain breaks: 1 Chain: "CP1" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1564 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 8, 'TRANS': 184} Chain breaks: 1 Chain: "DP1" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2299 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 4, 'TRANS': 268} Chain: "AP1" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "BP1" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.20 Number of scatterers: 14256 At special positions: 0 Unit cell: (124.8, 118.976, 143.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 7 15.00 O 2745 8.00 N 2423 7.00 C 9007 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 568.9 milliseconds 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 13 sheets defined 51.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'AP1' and resid 20 through 30 Processing helix chain 'AP1' and resid 35 through 37 No H-bonds generated for 'chain 'AP1' and resid 35 through 37' Processing helix chain 'AP1' and resid 38 through 61 removed outlier: 3.804A pdb=" N LEUAP1 59 " --> pdb=" O ARGAP1 55 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THRAP1 60 " --> pdb=" O TYRAP1 56 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASPAP1 61 " --> pdb=" O GLUAP1 57 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 62 through 66 Processing helix chain 'AP1' and resid 94 through 103 removed outlier: 4.076A pdb=" N LEUAP1 102 " --> pdb=" O LEUAP1 98 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 108 through 118 removed outlier: 3.742A pdb=" N LEUAP1 117 " --> pdb=" O PHEAP1 113 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLNAP1 118 " --> pdb=" O METAP1 114 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 132 through 138 Processing helix chain 'AP1' and resid 187 through 193 removed outlier: 3.934A pdb=" N THRAP1 190 " --> pdb=" O GLUAP1 187 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLUAP1 191 " --> pdb=" O ASPAP1 188 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 194 through 205 Processing helix chain 'AP1' and resid 292 through 296 Processing helix chain 'AP1' and resid 297 through 310 removed outlier: 3.596A pdb=" N TYRAP1 301 " --> pdb=" O THRAP1 297 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 345 through 349 Processing helix chain 'AP1' and resid 371 through 375 Processing helix chain 'AP1' and resid 398 through 420 removed outlier: 3.838A pdb=" N LYSAP1 402 " --> pdb=" O SERAP1 398 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 422 through 444 removed outlier: 6.724A pdb=" N LYSAP1 435 " --> pdb=" O GLUAP1 431 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASNAP1 436 " --> pdb=" O ALAAP1 432 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 447 through 453 removed outlier: 4.117A pdb=" N GLUAP1 453 " --> pdb=" O ARGAP1 449 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 460 through 463 removed outlier: 4.266A pdb=" N GLYAP1 463 " --> pdb=" O SERAP1 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'AP1' and resid 460 through 463' Processing helix chain 'AP1' and resid 468 through 476 Processing helix chain 'AP1' and resid 490 through 496 Processing helix chain 'AP1' and resid 500 through 506 Processing helix chain 'AP1' and resid 515 through 522 removed outlier: 3.813A pdb=" N GLUAP1 519 " --> pdb=" O GLUAP1 515 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYRAP1 520 " --> pdb=" O PROAP1 516 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 546 through 560 removed outlier: 3.667A pdb=" N ALAAP1 558 " --> pdb=" O GLUAP1 554 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 561 through 571 Processing helix chain 'AP1' and resid 599 through 608 Processing helix chain 'AP1' and resid 632 through 645 removed outlier: 3.580A pdb=" N GLUAP1 636 " --> pdb=" O HISAP1 632 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALAAP1 644 " --> pdb=" O GLNAP1 640 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASPAP1 645 " --> pdb=" O LYSAP1 641 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 648 through 666 removed outlier: 3.659A pdb=" N LYSAP1 652 " --> pdb=" O ASPAP1 648 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEUAP1 657 " --> pdb=" O ASPAP1 653 " (cutoff:3.500A) Processing helix chain 'AP1' and resid 672 through 689 removed outlier: 3.997A pdb=" N HISAP1 676 " --> pdb=" O ASPAP1 672 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 20 through 31 Processing helix chain 'BP1' and resid 35 through 37 No H-bonds generated for 'chain 'BP1' and resid 35 through 37' Processing helix chain 'BP1' and resid 38 through 61 removed outlier: 3.822A pdb=" N THRBP1 60 " --> pdb=" O TYRBP1 56 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 62 through 65 removed outlier: 3.899A pdb=" N LEUBP1 65 " --> pdb=" O PROBP1 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP1' and resid 62 through 65' Processing helix chain 'BP1' and resid 94 through 102 removed outlier: 3.522A pdb=" N LEUBP1 102 " --> pdb=" O LEUBP1 98 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 108 through 116 Processing helix chain 'BP1' and resid 132 through 138 Processing helix chain 'BP1' and resid 189 through 193 removed outlier: 4.135A pdb=" N TYRBP1 192 " --> pdb=" O GLNBP1 189 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 194 through 205 Processing helix chain 'BP1' and resid 297 through 309 Processing helix chain 'BP1' and resid 345 through 349 removed outlier: 4.301A pdb=" N LYSBP1 349 " --> pdb=" O ASNBP1 346 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 371 through 375 Processing helix chain 'BP1' and resid 397 through 399 No H-bonds generated for 'chain 'BP1' and resid 397 through 399' Processing helix chain 'BP1' and resid 400 through 420 removed outlier: 3.857A pdb=" N LYSBP1 406 " --> pdb=" O LYSBP1 402 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 422 through 444 removed outlier: 3.584A pdb=" N ALABP1 432 " --> pdb=" O LYSBP1 428 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LYSBP1 435 " --> pdb=" O GLUBP1 431 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ASNBP1 436 " --> pdb=" O ALABP1 432 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 447 through 453 removed outlier: 4.289A pdb=" N GLUBP1 453 " --> pdb=" O ARGBP1 449 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 469 through 475 Processing helix chain 'BP1' and resid 490 through 496 removed outlier: 3.841A pdb=" N ASNBP1 496 " --> pdb=" O GLUBP1 492 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 500 through 506 Processing helix chain 'BP1' and resid 516 through 525 removed outlier: 4.156A pdb=" N TYRBP1 520 " --> pdb=" O PROBP1 516 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLNBP1 524 " --> pdb=" O TYRBP1 520 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 546 through 571 removed outlier: 6.185A pdb=" N ASNBP1 562 " --> pdb=" O ALABP1 558 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEUBP1 563 " --> pdb=" O LYSBP1 559 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 599 through 608 Processing helix chain 'BP1' and resid 632 through 645 removed outlier: 3.906A pdb=" N GLUBP1 636 " --> pdb=" O HISBP1 632 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUBP1 638 " --> pdb=" O ILEBP1 634 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARGBP1 639 " --> pdb=" O VALBP1 635 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLNBP1 640 " --> pdb=" O GLUBP1 636 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYSBP1 641 " --> pdb=" O THRBP1 637 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASPBP1 645 " --> pdb=" O LYSBP1 641 " (cutoff:3.500A) Processing helix chain 'BP1' and resid 648 through 666 Processing helix chain 'BP1' and resid 672 through 689 removed outlier: 4.182A pdb=" N HISBP1 676 " --> pdb=" O ASPBP1 672 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 432 through 437 removed outlier: 3.772A pdb=" N GLNCP1 436 " --> pdb=" O HISCP1 432 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 441 through 462 removed outlier: 3.549A pdb=" N LEUCP1 459 " --> pdb=" O GLYCP1 455 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 470 through 474 removed outlier: 3.543A pdb=" N ILECP1 474 " --> pdb=" O SERCP1 471 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 513 through 519 Processing helix chain 'CP1' and resid 526 through 544 Processing helix chain 'CP1' and resid 553 through 564 removed outlier: 3.872A pdb=" N PHECP1 559 " --> pdb=" O ASPCP1 555 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 579 through 589 removed outlier: 3.559A pdb=" N ARGCP1 583 " --> pdb=" O LYSCP1 579 " (cutoff:3.500A) Processing helix chain 'CP1' and resid 598 through 612 removed outlier: 4.083A pdb=" N SERCP1 604 " --> pdb=" O PROCP1 600 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 24 through 74 removed outlier: 4.159A pdb=" N ARGDP1 30 " --> pdb=" O ALADP1 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRPDP1 31 " --> pdb=" O SERDP1 27 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HISDP1 33 " --> pdb=" O PHEDP1 29 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 77 through 112 removed outlier: 3.506A pdb=" N ALADP1 86 " --> pdb=" O GLUDP1 82 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 115 through 119 Processing helix chain 'DP1' and resid 141 through 155 removed outlier: 3.532A pdb=" N GLUDP1 145 " --> pdb=" O GLUDP1 141 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 155 through 164 Processing helix chain 'DP1' and resid 167 through 178 Processing helix chain 'DP1' and resid 179 through 182 Processing helix chain 'DP1' and resid 183 through 200 Processing helix chain 'DP1' and resid 202 through 227 removed outlier: 3.700A pdb=" N GLNDP1 212 " --> pdb=" O GLNDP1 208 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N METDP1 216 " --> pdb=" O GLNDP1 212 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLNDP1 217 " --> pdb=" O THRDP1 213 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHEDP1 218 " --> pdb=" O ILEDP1 214 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILEDP1 219 " --> pdb=" O VALDP1 215 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 229 through 233 Processing helix chain 'DP1' and resid 234 through 243 removed outlier: 4.271A pdb=" N PHEDP1 238 " --> pdb=" O PHEDP1 234 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THRDP1 239 " --> pdb=" O ARGDP1 235 " (cutoff:3.500A) Processing helix chain 'DP1' and resid 245 through 274 Processing sheet with id=AA1, first strand: chain 'AP1' and resid 12 through 16 removed outlier: 3.501A pdb=" N GLUAP1 13 " --> pdb=" O VALBP1 167 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYSBP1 142 " --> pdb=" O HISBP1 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THRBP1 85 " --> pdb=" O ILEBP1 76 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILEBP1 76 " --> pdb=" O THRBP1 85 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILEBP1 73 " --> pdb=" O THRBP1 214 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TYRBP1 216 " --> pdb=" O ILEBP1 73 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILEBP1 75 " --> pdb=" O TYRBP1 216 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N GLUBP1 218 " --> pdb=" O ILEBP1 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AP1' and resid 18 through 19 removed outlier: 6.836A pdb=" N GLNAP1 18 " --> pdb=" O ILEBP1 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'AP1' and resid 213 through 215 removed outlier: 4.108A pdb=" N LYSAP1 142 " --> pdb=" O HISAP1 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AP1' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'AP1' and resid 217 through 222 removed outlier: 3.512A pdb=" N LEUAP1 217 " --> pdb=" O ILEAP1 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYSAP1 219 " --> pdb=" O LYSAP1 275 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYSAP1 275 " --> pdb=" O LYSAP1 219 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARGAP1 221 " --> pdb=" O LYSAP1 273 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYSAP1 273 " --> pdb=" O ARGAP1 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AP1' and resid 361 through 363 removed outlier: 5.346A pdb=" N PHEAP1 361 " --> pdb=" O VALAP1 357 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VALAP1 357 " --> pdb=" O PHEAP1 361 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N METAP1 363 " --> pdb=" O LEUAP1 355 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASPAP1 382 " --> pdb=" O ARGAP1 330 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEAP1 329 " --> pdb=" O VALAP1 323 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALAAP1 317 " --> pdb=" O ILEAP1 335 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEUAP1 316 " --> pdb=" O VALDP1 129 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VALDP1 129 " --> pdb=" O LEUAP1 316 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VALAP1 318 " --> pdb=" O SERDP1 127 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SERDP1 127 " --> pdb=" O VALAP1 318 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N HISAP1 320 " --> pdb=" O SERDP1 125 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SERDP1 125 " --> pdb=" O HISAP1 320 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SERAP1 322 " --> pdb=" O GLYDP1 123 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AP1' and resid 457 through 458 Processing sheet with id=AA8, first strand: chain 'AP1' and resid 511 through 513 removed outlier: 8.927A pdb=" N VALAP1 511 " --> pdb=" O SERAP1 482 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYRAP1 484 " --> pdb=" O VALAP1 511 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N METAP1 513 " --> pdb=" O TYRAP1 484 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILEAP1 486 " --> pdb=" O METAP1 513 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILEAP1 483 " --> pdb=" O VALAP1 534 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AP1' and resid 578 through 579 removed outlier: 6.738A pdb=" N THRAP1 579 " --> pdb=" O ILEAP1 628 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'BP1' and resid 317 through 323 removed outlier: 3.997A pdb=" N ALABP1 317 " --> pdb=" O ILEBP1 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYSBP1 354 " --> pdb=" O GLYBP1 379 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEUBP1 355 " --> pdb=" O ILEBP1 362 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'BP1' and resid 467 through 468 removed outlier: 4.144A pdb=" N HISBP1 458 " --> pdb=" O TYRBP1 512 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N VALBP1 511 " --> pdb=" O SERBP1 482 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYRBP1 484 " --> pdb=" O VALBP1 511 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N METBP1 513 " --> pdb=" O TYRBP1 484 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILEBP1 486 " --> pdb=" O METBP1 513 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILEBP1 483 " --> pdb=" O VALBP1 534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'BP1' and resid 577 through 580 Processing sheet with id=AB4, first strand: chain 'CP1' and resid 475 through 477 removed outlier: 3.553A pdb=" N THRCP1 481 " --> pdb=" O HISCP1 477 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1932 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: 2.41 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3989 1.33 - 1.57: 10369 1.57 - 1.81: 140 1.81 - 2.05: 2 2.05 - 2.30: 1 Bond restraints: 14501 Sorted by residual: bond pdb=" CB PROCP1 524 " pdb=" CG PROCP1 524 " ideal model delta sigma weight residual 1.492 2.295 -0.803 5.00e-02 4.00e+02 2.58e+02 bond pdb=" CG PROCP1 524 " pdb=" CD PROCP1 524 " ideal model delta sigma weight residual 1.503 1.093 0.410 3.40e-02 8.65e+02 1.45e+02 bond pdb=" N PROCP1 524 " pdb=" CA PROCP1 524 " ideal model delta sigma weight residual 1.470 1.420 0.050 1.22e-02 6.72e+03 1.68e+01 bond pdb=" CB PROCP1 547 " pdb=" CG PROCP1 547 " ideal model delta sigma weight residual 1.492 1.643 -0.151 5.00e-02 4.00e+02 9.11e+00 bond pdb=" N PROCP1 524 " pdb=" CD PROCP1 524 " ideal model delta sigma weight residual 1.473 1.442 0.031 1.40e-02 5.10e+03 4.75e+00 ... (remaining 14496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.21: 19485 16.21 - 32.42: 3 32.42 - 48.63: 0 48.63 - 64.84: 0 64.84 - 81.05: 1 Bond angle restraints: 19489 Sorted by residual: angle pdb=" CB PROCP1 524 " pdb=" CG PROCP1 524 " pdb=" CD PROCP1 524 " ideal model delta sigma weight residual 106.10 25.05 81.05 3.20e+00 9.77e-02 6.41e+02 angle pdb=" CA PROCP1 524 " pdb=" N PROCP1 524 " pdb=" CD PROCP1 524 " ideal model delta sigma weight residual 112.00 81.60 30.40 1.40e+00 5.10e-01 4.72e+02 angle pdb=" N PROCP1 524 " pdb=" CD PROCP1 524 " pdb=" CG PROCP1 524 " ideal model delta sigma weight residual 103.20 122.45 -19.25 1.50e+00 4.44e-01 1.65e+02 angle pdb=" CA PROCP1 547 " pdb=" N PROCP1 547 " pdb=" CD PROCP1 547 " ideal model delta sigma weight residual 112.00 97.84 14.16 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PROCP1 524 " pdb=" CA PROCP1 524 " pdb=" CB PROCP1 524 " ideal model delta sigma weight residual 103.19 93.58 9.61 1.00e+00 1.00e+00 9.24e+01 ... (remaining 19484 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.93: 8235 26.93 - 53.87: 603 53.87 - 80.80: 91 80.80 - 107.74: 14 107.74 - 134.67: 1 Dihedral angle restraints: 8944 sinusoidal: 3819 harmonic: 5125 Sorted by residual: dihedral pdb=" N PROCP1 524 " pdb=" CG PROCP1 524 " pdb=" CD PROCP1 524 " pdb=" CB PROCP1 524 " ideal model delta sinusoidal sigma weight residual -30.00 -164.67 134.67 1 1.50e+01 4.44e-03 7.27e+01 dihedral pdb=" CA ASNBP1 30 " pdb=" C ASNBP1 30 " pdb=" N THRBP1 31 " pdb=" CA THRBP1 31 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA METBP1 567 " pdb=" C METBP1 567 " pdb=" N LYSBP1 568 " pdb=" CA LYSBP1 568 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 8941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1513 0.040 - 0.081: 473 0.081 - 0.121: 136 0.121 - 0.162: 11 0.162 - 0.202: 3 Chirality restraints: 2136 Sorted by residual: chirality pdb=" CA METBP1 567 " pdb=" N METBP1 567 " pdb=" C METBP1 567 " pdb=" CB METBP1 567 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CG LEUCP1 603 " pdb=" CB LEUCP1 603 " pdb=" CD1 LEUCP1 603 " pdb=" CD2 LEUCP1 603 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CG LEUBP1 654 " pdb=" CB LEUBP1 654 " pdb=" CD1 LEUBP1 654 " pdb=" CD2 LEUBP1 654 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 2133 not shown) Planarity restraints: 2486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEUCP1 546 " 0.098 5.00e-02 4.00e+02 1.37e-01 2.99e+01 pdb=" N PROCP1 547 " -0.236 5.00e-02 4.00e+02 pdb=" CA PROCP1 547 " 0.067 5.00e-02 4.00e+02 pdb=" CD PROCP1 547 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARGCP1 596 " -0.075 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PROCP1 597 " 0.189 5.00e-02 4.00e+02 pdb=" CA PROCP1 597 " -0.054 5.00e-02 4.00e+02 pdb=" CD PROCP1 597 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASNCP1 523 " -0.073 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PROCP1 524 " 0.159 5.00e-02 4.00e+02 pdb=" CA PROCP1 524 " -0.031 5.00e-02 4.00e+02 pdb=" CD PROCP1 524 " -0.056 5.00e-02 4.00e+02 ... (remaining 2483 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 510 2.71 - 3.26: 15103 3.26 - 3.81: 23943 3.81 - 4.35: 29984 4.35 - 4.90: 48976 Nonbonded interactions: 118516 Sorted by model distance: nonbonded pdb=" O ASNAP1 100 " pdb=" OG1 THRAP1 104 " model vdw 2.163 3.040 nonbonded pdb=" O ARGBP1 449 " pdb=" NH1 ARGBP1 449 " model vdw 2.211 3.120 nonbonded pdb=" N GLUBP1 218 " pdb=" OE1 GLUBP1 218 " model vdw 2.224 3.120 nonbonded pdb=" OE1 GLUBP1 281 " pdb=" NZ LYSBP1 284 " model vdw 2.234 3.120 nonbonded pdb=" O LEUCP1 546 " pdb=" OG SERCP1 549 " model vdw 2.235 3.040 ... (remaining 118511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'AP1' and (resid 10 through 690 or resid 801)) selection = (chain 'BP1' and (resid 10 through 223 or resid 270 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.803 14501 Z= 0.238 Angle : 0.977 81.046 19489 Z= 0.474 Chirality : 0.042 0.202 2136 Planarity : 0.006 0.137 2486 Dihedral : 18.239 134.675 5614 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.64 % Favored : 95.18 % Rotamer: Outliers : 0.25 % Allowed : 25.59 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.20), residues: 1723 helix: 0.76 (0.18), residues: 790 sheet: -0.72 (0.37), residues: 205 loop : -1.06 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGDP1 52 TYR 0.051 0.002 TYRAP1 681 PHE 0.024 0.002 PHEAP1 32 TRP 0.025 0.002 TRPDP1 193 HIS 0.008 0.001 HISCP1 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00844 / 0.24 (14501) covalent geometry : angle 0.97710 / 0.47 (19489) hydrogen bonds : bond 0.16650 / 10.94 ( 686) hydrogen bonds : angle 6.41323 / 4.30 ( 1932) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8848 (tt) REVERT: AP1 114 MET cc_start: 0.7483 (mmm) cc_final: 0.7114 (mmm) REVERT: AP1 623 LYS cc_start: 0.7986 (pttm) cc_final: 0.7520 (mmtm) REVERT: BP1 606 MET cc_start: 0.8144 (mmm) cc_final: 0.7934 (mmm) REVERT: BP1 654 LEU cc_start: 0.9265 (mm) cc_final: 0.9055 (mm) REVERT: CP1 519 MET cc_start: 0.3612 (mtt) cc_final: 0.3332 (mtt) REVERT: DP1 162 PHE cc_start: 0.7328 (t80) cc_final: 0.7003 (m-80) REVERT: DP1 218 PHE cc_start: 0.7845 (m-80) cc_final: 0.7542 (m-80) outliers start: 4 outliers final: 1 residues processed: 206 average time/residue: 0.1295 time to fit residues: 38.1463 Evaluate side-chains 196 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain CP1 residue 466 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.128157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095088 restraints weight = 34025.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.095170 restraints weight = 21760.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096350 restraints weight = 16625.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096460 restraints weight = 15985.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.096428 restraints weight = 13833.334| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14501 Z= 0.142 Angle : 0.593 8.505 19489 Z= 0.311 Chirality : 0.042 0.235 2136 Planarity : 0.005 0.122 2486 Dihedral : 5.104 68.930 1899 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 2.92 % Allowed : 22.22 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1723 helix: 1.11 (0.19), residues: 780 sheet: -0.45 (0.37), residues: 211 loop : -0.92 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGDP1 52 TYR 0.037 0.002 TYRAP1 681 PHE 0.017 0.001 PHEBP1 329 TRP 0.019 0.002 TRPBP1 157 HIS 0.005 0.001 HISCP1 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (14501) covalent geometry : angle 0.59263 / 0.31 (19489) hydrogen bonds : bond 0.03961 / 2.60 ( 686) hydrogen bonds : angle 4.87589 / 3.26 ( 1932) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 32 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8583 (t80) REVERT: AP1 40 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8772 (tt) REVERT: AP1 114 MET cc_start: 0.7416 (mmm) cc_final: 0.7060 (mmm) REVERT: AP1 310 ASN cc_start: 0.7882 (t0) cc_final: 0.7441 (t0) REVERT: AP1 603 GLU cc_start: 0.8642 (tp30) cc_final: 0.8305 (tp30) REVERT: AP1 623 LYS cc_start: 0.7996 (pttm) cc_final: 0.7491 (ttpp) REVERT: AP1 681 TYR cc_start: 0.8533 (m-80) cc_final: 0.8176 (m-80) REVERT: BP1 385 ASP cc_start: 0.7762 (p0) cc_final: 0.7552 (p0) REVERT: BP1 538 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8648 (mtpm) REVERT: BP1 553 MET cc_start: 0.9205 (mmm) cc_final: 0.8906 (mmm) REVERT: DP1 211 HIS cc_start: 0.0279 (t-90) cc_final: -0.0360 (m90) REVERT: DP1 218 PHE cc_start: 0.7839 (m-80) cc_final: 0.7501 (m-80) REVERT: DP1 259 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.6917 (t80) outliers start: 46 outliers final: 22 residues processed: 247 average time/residue: 0.1193 time to fit residues: 42.0351 Evaluate side-chains 225 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 32 PHE Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 589 CYS Chi-restraints excluded: chain BP1 residue 60 THR Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 464 ASP Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 572 ASP Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 482 VAL Chi-restraints excluded: chain CP1 residue 484 ILE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain CP1 residue 603 LEU Chi-restraints excluded: chain DP1 residue 228 VAL Chi-restraints excluded: chain DP1 residue 259 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 169 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.0030 chunk 17 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.129419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092739 restraints weight = 34284.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.095504 restraints weight = 20052.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.097320 restraints weight = 14460.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.098428 restraints weight = 11911.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.098924 restraints weight = 10669.853| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14501 Z= 0.109 Angle : 0.543 7.132 19489 Z= 0.282 Chirality : 0.041 0.245 2136 Planarity : 0.004 0.056 2486 Dihedral : 4.959 71.135 1899 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 3.43 % Allowed : 21.90 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.21), residues: 1723 helix: 1.30 (0.19), residues: 774 sheet: -0.45 (0.36), residues: 211 loop : -0.84 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGDP1 52 TYR 0.026 0.001 TYRAP1 681 PHE 0.014 0.001 PHEAP1 32 TRP 0.025 0.002 TRPCP1 423 HIS 0.004 0.001 HISAP1 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (14501) covalent geometry : angle 0.54312 / 0.28 (19489) hydrogen bonds : bond 0.03550 / 2.33 ( 686) hydrogen bonds : angle 4.52874 / 3.04 ( 1932) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 230 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8770 (tt) REVERT: AP1 310 ASN cc_start: 0.7777 (t0) cc_final: 0.7354 (t0) REVERT: AP1 603 GLU cc_start: 0.8610 (tp30) cc_final: 0.8250 (tp30) REVERT: AP1 681 TYR cc_start: 0.8477 (m-80) cc_final: 0.7976 (m-80) REVERT: BP1 280 GLU cc_start: 0.6150 (OUTLIER) cc_final: 0.5938 (tt0) REVERT: BP1 385 ASP cc_start: 0.7695 (p0) cc_final: 0.7460 (p0) REVERT: BP1 538 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8613 (mtpm) REVERT: BP1 553 MET cc_start: 0.9064 (mmm) cc_final: 0.8776 (mmm) REVERT: CP1 469 MET cc_start: 0.8680 (tmm) cc_final: 0.8273 (tmm) REVERT: CP1 607 GLU cc_start: 0.9068 (tp30) cc_final: 0.8835 (tp30) REVERT: DP1 218 PHE cc_start: 0.7642 (m-80) cc_final: 0.7365 (m-80) outliers start: 54 outliers final: 28 residues processed: 265 average time/residue: 0.1355 time to fit residues: 51.5130 Evaluate side-chains 229 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 589 CYS Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 280 GLU Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 572 ASP Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 482 VAL Chi-restraints excluded: chain CP1 residue 489 LEU Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain CP1 residue 603 LEU Chi-restraints excluded: chain DP1 residue 190 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 129 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 171 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.129155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.094718 restraints weight = 34002.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096318 restraints weight = 21496.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.096118 restraints weight = 15071.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096680 restraints weight = 16500.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096572 restraints weight = 14411.696| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14501 Z= 0.127 Angle : 0.553 7.746 19489 Z= 0.286 Chirality : 0.041 0.252 2136 Planarity : 0.004 0.051 2486 Dihedral : 4.967 71.871 1899 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Rotamer: Outliers : 3.24 % Allowed : 22.48 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1723 helix: 1.27 (0.19), residues: 776 sheet: -0.46 (0.37), residues: 208 loop : -0.76 (0.24), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGBP1 449 TYR 0.019 0.001 TYRAP1 681 PHE 0.019 0.001 PHEAP1 32 TRP 0.040 0.002 TRPDP1 98 HIS 0.003 0.001 HISAP1 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14501) covalent geometry : angle 0.55278 / 0.29 (19489) hydrogen bonds : bond 0.03421 / 2.24 ( 686) hydrogen bonds : angle 4.47928 / 3.01 ( 1932) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8753 (tt) REVERT: AP1 310 ASN cc_start: 0.7897 (t0) cc_final: 0.7443 (t0) REVERT: AP1 603 GLU cc_start: 0.8609 (tp30) cc_final: 0.8252 (tp30) REVERT: AP1 681 TYR cc_start: 0.8571 (m-80) cc_final: 0.8101 (m-80) REVERT: BP1 385 ASP cc_start: 0.7758 (p0) cc_final: 0.7500 (p0) REVERT: BP1 538 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8584 (mtpm) REVERT: BP1 617 MET cc_start: 0.8317 (ppp) cc_final: 0.8049 (ppp) REVERT: CP1 469 MET cc_start: 0.8839 (tmm) cc_final: 0.8489 (tmm) REVERT: DP1 162 PHE cc_start: 0.7479 (t80) cc_final: 0.6427 (t80) REVERT: DP1 211 HIS cc_start: -0.0166 (t-90) cc_final: -0.0393 (m-70) REVERT: DP1 218 PHE cc_start: 0.7749 (m-80) cc_final: 0.7445 (m-80) REVERT: DP1 231 ARG cc_start: 0.0751 (OUTLIER) cc_final: 0.0102 (ptt-90) REVERT: DP1 247 GLN cc_start: 0.2979 (pt0) cc_final: 0.2464 (tp40) REVERT: DP1 249 MET cc_start: 0.3747 (tpp) cc_final: 0.3526 (tpp) outliers start: 51 outliers final: 32 residues processed: 249 average time/residue: 0.1244 time to fit residues: 44.4331 Evaluate side-chains 235 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 589 CYS Chi-restraints excluded: chain AP1 residue 671 GLU Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 572 ASP Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 482 VAL Chi-restraints excluded: chain CP1 residue 489 LEU Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain CP1 residue 603 LEU Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 228 VAL Chi-restraints excluded: chain DP1 residue 231 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 122 optimal weight: 8.9990 chunk 74 optimal weight: 0.0020 chunk 149 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 8.9990 chunk 17 optimal weight: 0.3980 chunk 83 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.129823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098306 restraints weight = 34387.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.097725 restraints weight = 21098.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098075 restraints weight = 20032.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.098503 restraints weight = 15404.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098667 restraints weight = 14250.474| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14501 Z= 0.108 Angle : 0.537 7.413 19489 Z= 0.276 Chirality : 0.041 0.256 2136 Planarity : 0.004 0.048 2486 Dihedral : 4.873 71.962 1899 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.71 % Favored : 96.11 % Rotamer: Outliers : 3.05 % Allowed : 22.54 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.21), residues: 1723 helix: 1.26 (0.19), residues: 787 sheet: -0.44 (0.36), residues: 208 loop : -0.75 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGDP1 92 TYR 0.018 0.001 TYRCP1 532 PHE 0.016 0.001 PHEAP1 329 TRP 0.028 0.002 TRPBP1 157 HIS 0.003 0.001 HISAP1 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14501) covalent geometry : angle 0.53666 / 0.28 (19489) hydrogen bonds : bond 0.03230 / 2.12 ( 686) hydrogen bonds : angle 4.34531 / 2.94 ( 1932) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8706 (tt) REVERT: AP1 310 ASN cc_start: 0.7858 (t0) cc_final: 0.7425 (t0) REVERT: AP1 681 TYR cc_start: 0.8493 (m-80) cc_final: 0.8006 (m-80) REVERT: BP1 335 ILE cc_start: 0.8298 (mp) cc_final: 0.8057 (mt) REVERT: BP1 385 ASP cc_start: 0.7714 (p0) cc_final: 0.7445 (p0) REVERT: BP1 431 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6864 (tm-30) REVERT: BP1 538 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8631 (mtpm) REVERT: BP1 553 MET cc_start: 0.9290 (mmm) cc_final: 0.8863 (mmm) REVERT: BP1 617 MET cc_start: 0.8263 (ppp) cc_final: 0.7975 (ppp) REVERT: BP1 649 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8737 (tppt) REVERT: CP1 469 MET cc_start: 0.8779 (tmm) cc_final: 0.8519 (tmm) REVERT: CP1 583 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8931 (mmt-90) REVERT: DP1 162 PHE cc_start: 0.7473 (t80) cc_final: 0.6371 (t80) REVERT: DP1 218 PHE cc_start: 0.7593 (m-80) cc_final: 0.7311 (m-80) REVERT: DP1 231 ARG cc_start: 0.1132 (OUTLIER) cc_final: 0.0622 (ptt180) REVERT: DP1 247 GLN cc_start: 0.2656 (pt0) cc_final: 0.1694 (tp40) REVERT: DP1 250 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8332 (pt0) outliers start: 48 outliers final: 30 residues processed: 251 average time/residue: 0.1197 time to fit residues: 43.0149 Evaluate side-chains 237 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 589 CYS Chi-restraints excluded: chain AP1 residue 620 MET Chi-restraints excluded: chain AP1 residue 671 GLU Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 457 TYR Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 489 LEU Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 231 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.124146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.086496 restraints weight = 34198.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089109 restraints weight = 20292.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090626 restraints weight = 14850.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091774 restraints weight = 12441.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092255 restraints weight = 11205.854| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14501 Z= 0.266 Angle : 0.659 14.956 19489 Z= 0.340 Chirality : 0.044 0.144 2136 Planarity : 0.004 0.049 2486 Dihedral : 5.333 75.355 1899 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.46 % Favored : 94.37 % Rotamer: Outliers : 2.98 % Allowed : 24.00 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.21), residues: 1723 helix: 1.10 (0.19), residues: 787 sheet: -0.64 (0.36), residues: 210 loop : -0.86 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGDP1 52 TYR 0.020 0.002 TYRBP1 681 PHE 0.030 0.002 PHEAP1 32 TRP 0.038 0.003 TRPBP1 157 HIS 0.007 0.001 HISAP1 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.27 (14501) covalent geometry : angle 0.65878 / 0.34 (19489) hydrogen bonds : bond 0.03704 / 2.43 ( 686) hydrogen bonds : angle 4.70066 / 3.17 ( 1932) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8956 (tt) REVERT: AP1 310 ASN cc_start: 0.7892 (t0) cc_final: 0.7415 (t0) REVERT: AP1 492 GLU cc_start: 0.7970 (pm20) cc_final: 0.7689 (pm20) REVERT: AP1 542 GLU cc_start: 0.8059 (tp30) cc_final: 0.7753 (tt0) REVERT: AP1 681 TYR cc_start: 0.8616 (m-80) cc_final: 0.8154 (m-80) REVERT: BP1 385 ASP cc_start: 0.7976 (p0) cc_final: 0.7771 (p0) REVERT: BP1 553 MET cc_start: 0.9186 (mmm) cc_final: 0.8901 (mmm) REVERT: BP1 649 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8742 (tppt) REVERT: CP1 469 MET cc_start: 0.8869 (tmm) cc_final: 0.8331 (tmm) REVERT: DP1 218 PHE cc_start: 0.7712 (m-80) cc_final: 0.7472 (m-80) REVERT: DP1 231 ARG cc_start: 0.1669 (OUTLIER) cc_final: 0.0472 (ptt180) REVERT: DP1 247 GLN cc_start: 0.2884 (pt0) cc_final: 0.2155 (tp40) outliers start: 47 outliers final: 35 residues processed: 231 average time/residue: 0.1104 time to fit residues: 37.1643 Evaluate side-chains 220 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 131 VAL Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 363 MET Chi-restraints excluded: chain AP1 residue 374 LEU Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 476 MET Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 534 VAL Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 589 CYS Chi-restraints excluded: chain AP1 residue 682 ARG Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 352 ASN Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 484 ILE Chi-restraints excluded: chain CP1 residue 541 LEU Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 228 VAL Chi-restraints excluded: chain DP1 residue 231 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 82 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 83 optimal weight: 0.0370 chunk 158 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.127489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090228 restraints weight = 33734.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.092967 restraints weight = 19795.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094708 restraints weight = 14360.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095666 restraints weight = 11910.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.095882 restraints weight = 10718.032| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14501 Z= 0.123 Angle : 0.582 12.024 19489 Z= 0.297 Chirality : 0.041 0.170 2136 Planarity : 0.004 0.050 2486 Dihedral : 5.108 77.002 1899 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.89 % Favored : 95.94 % Rotamer: Outliers : 2.54 % Allowed : 24.57 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1723 helix: 1.20 (0.19), residues: 784 sheet: -0.60 (0.37), residues: 210 loop : -0.75 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGDP1 52 TYR 0.019 0.002 TYRDP1 174 PHE 0.018 0.001 PHEAP1 32 TRP 0.046 0.002 TRPBP1 157 HIS 0.004 0.001 HISAP1 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14501) covalent geometry : angle 0.58249 / 0.30 (19489) hydrogen bonds : bond 0.03350 / 2.19 ( 686) hydrogen bonds : angle 4.45300 / 3.00 ( 1932) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8823 (tt) REVERT: AP1 310 ASN cc_start: 0.7880 (t0) cc_final: 0.7395 (t0) REVERT: AP1 346 ASN cc_start: 0.6981 (t0) cc_final: 0.6723 (t0) REVERT: AP1 524 GLN cc_start: 0.8570 (mp10) cc_final: 0.8176 (mp10) REVERT: AP1 542 GLU cc_start: 0.7921 (tp30) cc_final: 0.7573 (tt0) REVERT: AP1 681 TYR cc_start: 0.8565 (m-10) cc_final: 0.8056 (m-80) REVERT: BP1 335 ILE cc_start: 0.8391 (mp) cc_final: 0.8160 (mt) REVERT: BP1 385 ASP cc_start: 0.7782 (p0) cc_final: 0.7532 (p0) REVERT: BP1 431 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6923 (tm-30) REVERT: BP1 538 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8828 (mtpt) REVERT: BP1 553 MET cc_start: 0.9197 (mmm) cc_final: 0.8898 (mmm) REVERT: DP1 98 TRP cc_start: 0.6921 (t-100) cc_final: 0.6548 (t-100) REVERT: DP1 112 MET cc_start: 0.8936 (tpp) cc_final: 0.8563 (tpp) REVERT: DP1 162 PHE cc_start: 0.7548 (t80) cc_final: 0.6368 (t80) REVERT: DP1 211 HIS cc_start: -0.0421 (t-90) cc_final: -0.0869 (t-90) REVERT: DP1 218 PHE cc_start: 0.7732 (m-80) cc_final: 0.7507 (m-80) REVERT: DP1 231 ARG cc_start: 0.1468 (OUTLIER) cc_final: 0.1042 (ptt180) outliers start: 40 outliers final: 30 residues processed: 232 average time/residue: 0.1121 time to fit residues: 37.8771 Evaluate side-chains 228 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 363 MET Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 476 MET Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 457 TYR Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 519 MET Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 228 VAL Chi-restraints excluded: chain DP1 residue 231 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 101 optimal weight: 0.2980 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.127598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090196 restraints weight = 33872.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.092946 restraints weight = 19857.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094684 restraints weight = 14404.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095841 restraints weight = 11920.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.096235 restraints weight = 10679.188| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14501 Z= 0.133 Angle : 0.609 11.104 19489 Z= 0.307 Chirality : 0.041 0.228 2136 Planarity : 0.004 0.052 2486 Dihedral : 5.070 76.669 1899 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.70 % Favored : 95.12 % Rotamer: Outliers : 2.60 % Allowed : 25.02 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.21), residues: 1723 helix: 1.16 (0.19), residues: 785 sheet: -0.60 (0.37), residues: 210 loop : -0.73 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGBP1 449 TYR 0.020 0.002 TYRAP1 619 PHE 0.019 0.001 PHEAP1 32 TRP 0.049 0.002 TRPBP1 157 HIS 0.004 0.001 HISAP1 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (14501) covalent geometry : angle 0.60851 / 0.31 (19489) hydrogen bonds : bond 0.03331 / 2.17 ( 686) hydrogen bonds : angle 4.44255 / 2.99 ( 1932) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8835 (tt) REVERT: AP1 114 MET cc_start: 0.7534 (mmm) cc_final: 0.6962 (mmm) REVERT: AP1 310 ASN cc_start: 0.7920 (t0) cc_final: 0.7432 (t0) REVERT: AP1 346 ASN cc_start: 0.6978 (t0) cc_final: 0.6710 (t0) REVERT: AP1 542 GLU cc_start: 0.7967 (tp30) cc_final: 0.7627 (tt0) REVERT: AP1 619 TYR cc_start: 0.6422 (t80) cc_final: 0.6047 (t80) REVERT: AP1 681 TYR cc_start: 0.8584 (m-10) cc_final: 0.8107 (m-80) REVERT: BP1 385 ASP cc_start: 0.7791 (p0) cc_final: 0.7573 (p0) REVERT: BP1 431 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6972 (tm-30) REVERT: BP1 538 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8862 (mtpt) REVERT: CP1 469 MET cc_start: 0.8911 (tmm) cc_final: 0.8340 (tmm) REVERT: CP1 512 MET cc_start: 0.5333 (mpp) cc_final: 0.4748 (mtm) REVERT: DP1 98 TRP cc_start: 0.7053 (t-100) cc_final: 0.6665 (t-100) REVERT: DP1 112 MET cc_start: 0.8948 (tpp) cc_final: 0.8521 (tpp) REVERT: DP1 162 PHE cc_start: 0.7538 (t80) cc_final: 0.6304 (t80) REVERT: DP1 211 HIS cc_start: -0.0463 (t-90) cc_final: -0.0829 (t-90) REVERT: DP1 218 PHE cc_start: 0.7680 (m-80) cc_final: 0.7446 (m-80) REVERT: DP1 231 ARG cc_start: 0.1420 (OUTLIER) cc_final: 0.1108 (ptt180) REVERT: DP1 247 GLN cc_start: 0.3073 (pt0) cc_final: 0.2610 (tp40) outliers start: 41 outliers final: 30 residues processed: 227 average time/residue: 0.1043 time to fit residues: 34.5860 Evaluate side-chains 231 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 363 MET Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 476 MET Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 671 GLU Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 457 TYR Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 519 MET Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 231 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 81 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 79 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.090914 restraints weight = 33816.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093637 restraints weight = 19834.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.095423 restraints weight = 14341.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.096553 restraints weight = 11834.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097051 restraints weight = 10590.617| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14501 Z= 0.127 Angle : 0.625 10.679 19489 Z= 0.311 Chirality : 0.041 0.195 2136 Planarity : 0.004 0.072 2486 Dihedral : 5.059 76.567 1899 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.24 % Favored : 95.59 % Rotamer: Outliers : 2.35 % Allowed : 25.21 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1723 helix: 1.17 (0.19), residues: 783 sheet: -0.57 (0.37), residues: 210 loop : -0.71 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARGDP1 55 TYR 0.018 0.002 TYRAP1 619 PHE 0.021 0.001 PHEAP1 32 TRP 0.044 0.002 TRPBP1 157 HIS 0.004 0.001 HISAP1 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (14501) covalent geometry : angle 0.62549 / 0.31 (19489) hydrogen bonds : bond 0.03282 / 2.15 ( 686) hydrogen bonds : angle 4.40479 / 2.97 ( 1932) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8820 (tt) REVERT: AP1 310 ASN cc_start: 0.7879 (t0) cc_final: 0.7405 (t0) REVERT: AP1 346 ASN cc_start: 0.6945 (t0) cc_final: 0.6664 (t0) REVERT: AP1 524 GLN cc_start: 0.8519 (mp10) cc_final: 0.8314 (mp10) REVERT: AP1 542 GLU cc_start: 0.7955 (tp30) cc_final: 0.7573 (tt0) REVERT: AP1 553 MET cc_start: 0.9213 (mmt) cc_final: 0.8671 (mmt) REVERT: AP1 617 MET cc_start: 0.7836 (tmm) cc_final: 0.7500 (tmm) REVERT: AP1 681 TYR cc_start: 0.8543 (m-10) cc_final: 0.8145 (m-80) REVERT: BP1 335 ILE cc_start: 0.8301 (mp) cc_final: 0.7995 (mt) REVERT: BP1 538 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8885 (mtpt) REVERT: BP1 553 MET cc_start: 0.8990 (mmm) cc_final: 0.8767 (mmm) REVERT: CP1 469 MET cc_start: 0.8915 (tmm) cc_final: 0.8355 (tmm) REVERT: CP1 512 MET cc_start: 0.5302 (mpp) cc_final: 0.4723 (mtm) REVERT: DP1 112 MET cc_start: 0.8976 (tpp) cc_final: 0.8548 (tpp) REVERT: DP1 162 PHE cc_start: 0.7496 (t80) cc_final: 0.6203 (t80) REVERT: DP1 211 HIS cc_start: -0.0629 (t-90) cc_final: -0.0970 (t-170) REVERT: DP1 218 PHE cc_start: 0.7612 (m-80) cc_final: 0.7382 (m-80) REVERT: DP1 231 ARG cc_start: 0.1503 (OUTLIER) cc_final: 0.0959 (ptt180) REVERT: DP1 247 GLN cc_start: 0.3021 (pt0) cc_final: 0.2543 (tp40) outliers start: 37 outliers final: 30 residues processed: 232 average time/residue: 0.1224 time to fit residues: 40.5768 Evaluate side-chains 234 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 126 ILE Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 363 MET Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 476 MET Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain AP1 residue 620 MET Chi-restraints excluded: chain BP1 residue 60 THR Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 457 TYR Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 538 LYS Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 519 MET Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 231 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 0.0040 chunk 153 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 overall best weight: 2.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.121751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082963 restraints weight = 33796.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.085717 restraints weight = 19292.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.087495 restraints weight = 13788.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088636 restraints weight = 11324.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.089141 restraints weight = 10112.607| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 14501 Z= 0.264 Angle : 0.711 12.142 19489 Z= 0.362 Chirality : 0.044 0.222 2136 Planarity : 0.005 0.056 2486 Dihedral : 5.460 77.495 1899 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.09 % Favored : 93.73 % Rotamer: Outliers : 2.29 % Allowed : 25.21 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1723 helix: 0.99 (0.19), residues: 783 sheet: -0.84 (0.36), residues: 211 loop : -0.82 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARGDP1 55 TYR 0.026 0.002 TYRBP1 681 PHE 0.030 0.002 PHEAP1 32 TRP 0.040 0.003 TRPBP1 157 HIS 0.007 0.001 HISAP1 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 (14501) covalent geometry : angle 0.71113 / 0.36 (19489) hydrogen bonds : bond 0.03692 / 2.42 ( 686) hydrogen bonds : angle 4.71429 / 3.18 ( 1932) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3446 Ramachandran restraints generated. 1723 Oldfield, 0 Emsley, 1723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AP1 40 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8969 (tt) REVERT: AP1 346 ASN cc_start: 0.7063 (t0) cc_final: 0.6822 (t0) REVERT: AP1 553 MET cc_start: 0.9312 (mmt) cc_final: 0.8757 (mmt) REVERT: AP1 617 MET cc_start: 0.8041 (tmm) cc_final: 0.7645 (tmm) REVERT: AP1 681 TYR cc_start: 0.8660 (m-10) cc_final: 0.8256 (m-80) REVERT: BP1 171 HIS cc_start: 0.7773 (m-70) cc_final: 0.7568 (m90) REVERT: BP1 553 MET cc_start: 0.9026 (mmm) cc_final: 0.8782 (mmm) REVERT: CP1 469 MET cc_start: 0.9031 (tmm) cc_final: 0.8511 (tmm) REVERT: CP1 512 MET cc_start: 0.5249 (mpp) cc_final: 0.4734 (mtm) REVERT: DP1 98 TRP cc_start: 0.6947 (t-100) cc_final: 0.6423 (t-100) REVERT: DP1 112 MET cc_start: 0.8929 (tpp) cc_final: 0.8597 (tpp) REVERT: DP1 218 PHE cc_start: 0.7778 (m-80) cc_final: 0.7554 (m-80) REVERT: DP1 247 GLN cc_start: 0.3396 (pt0) cc_final: 0.2871 (tp40) outliers start: 36 outliers final: 31 residues processed: 212 average time/residue: 0.1146 time to fit residues: 35.2724 Evaluate side-chains 210 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AP1 residue 40 LEU Chi-restraints excluded: chain AP1 residue 93 MET Chi-restraints excluded: chain AP1 residue 135 SER Chi-restraints excluded: chain AP1 residue 318 VAL Chi-restraints excluded: chain AP1 residue 360 VAL Chi-restraints excluded: chain AP1 residue 363 MET Chi-restraints excluded: chain AP1 residue 374 LEU Chi-restraints excluded: chain AP1 residue 417 SER Chi-restraints excluded: chain AP1 residue 521 CYS Chi-restraints excluded: chain AP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 60 THR Chi-restraints excluded: chain BP1 residue 114 MET Chi-restraints excluded: chain BP1 residue 181 VAL Chi-restraints excluded: chain BP1 residue 213 ILE Chi-restraints excluded: chain BP1 residue 272 ILE Chi-restraints excluded: chain BP1 residue 277 ILE Chi-restraints excluded: chain BP1 residue 278 ASP Chi-restraints excluded: chain BP1 residue 352 ASN Chi-restraints excluded: chain BP1 residue 369 LEU Chi-restraints excluded: chain BP1 residue 460 SER Chi-restraints excluded: chain BP1 residue 521 CYS Chi-restraints excluded: chain BP1 residue 584 LEU Chi-restraints excluded: chain BP1 residue 658 LEU Chi-restraints excluded: chain BP1 residue 686 LEU Chi-restraints excluded: chain CP1 residue 447 ASP Chi-restraints excluded: chain CP1 residue 466 HIS Chi-restraints excluded: chain CP1 residue 519 MET Chi-restraints excluded: chain CP1 residue 559 PHE Chi-restraints excluded: chain CP1 residue 587 ASP Chi-restraints excluded: chain CP1 residue 592 VAL Chi-restraints excluded: chain DP1 residue 190 LEU Chi-restraints excluded: chain DP1 residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 122 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.125108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086464 restraints weight = 33291.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.089339 restraints weight = 18850.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091034 restraints weight = 13408.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092366 restraints weight = 11015.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092879 restraints weight = 9760.528| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14501 Z= 0.132 Angle : 0.664 11.091 19489 Z= 0.333 Chirality : 0.042 0.185 2136 Planarity : 0.004 0.068 2486 Dihedral : 5.229 79.520 1899 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.29 % Favored : 95.59 % Rotamer: Outliers : 2.03 % Allowed : 26.03 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.21), residues: 1723 helix: 1.00 (0.19), residues: 787 sheet: -0.73 (0.37), residues: 211 loop : -0.74 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGDP1 55 TYR 0.018 0.002 TYRBP1 681 PHE 0.024 0.001 PHEAP1 32 TRP 0.043 0.003 TRPBP1 157 HIS 0.004 0.001 HISAP1 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (14501) covalent geometry : angle 0.66436 / 0.33 (19489) hydrogen bonds : bond 0.03353 / 2.19 ( 686) hydrogen bonds : angle 4.51204 / 3.05 ( 1932) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2494.31 seconds wall clock time: 43 minutes 33.02 seconds (2613.02 seconds total)