Starting phenix.real_space_refine on Thu Feb 5 10:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lpk_63270/02_2026/9lpk_63270.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lpk_63270/02_2026/9lpk_63270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lpk_63270/02_2026/9lpk_63270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lpk_63270/02_2026/9lpk_63270.map" model { file = "/net/cci-nas-00/data/ceres_data/9lpk_63270/02_2026/9lpk_63270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lpk_63270/02_2026/9lpk_63270.cif" } resolution = 3.03 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= 0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10381 2.51 5 N 2731 2.21 5 O 3066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16278 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1604 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 12, 'TRANS': 190} Chain breaks: 1 Chain: "C" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5364 Classifications: {'peptide': 685} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 42, 'TRANS': 642} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5358 Classifications: {'peptide': 684} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 42, 'TRANS': 641} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1174 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "D" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1174 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "F" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1604 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 12, 'TRANS': 190} Chain breaks: 1 Time building chain proxies: 3.77, per 1000 atoms: 0.23 Number of scatterers: 16278 At special positions: 0 Unit cell: (139.7, 152.9, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3066 8.00 N 2731 7.00 C 10381 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: 1.01 Conformation dependent library (CDL) restraints added in 605.0 milliseconds 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3862 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 31 sheets defined 25.7% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 432 through 439 removed outlier: 3.625A pdb=" N VAL A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.791A pdb=" N SER A 529 " --> pdb=" O ASP A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.636A pdb=" N LYS C 145 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 146 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 147 " --> pdb=" O ALA C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 147' Processing helix chain 'C' and resid 164 through 168 Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.695A pdb=" N THR C 187 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.543A pdb=" N LYS C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 328 through 339 Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.937A pdb=" N SER C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 394 " --> pdb=" O MET C 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 389 through 394' Processing helix chain 'C' and resid 453 through 463 removed outlier: 4.159A pdb=" N GLN C 463 " --> pdb=" O PHE C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 483 removed outlier: 3.954A pdb=" N GLU C 483 " --> pdb=" O HIS C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 483' Processing helix chain 'C' and resid 506 through 520 removed outlier: 3.643A pdb=" N CYS C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 removed outlier: 3.559A pdb=" N ASN C 539 " --> pdb=" O GLN C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 551 Processing helix chain 'C' and resid 553 through 578 Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 600 through 604 Processing helix chain 'C' and resid 642 through 652 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 688 through 692 removed outlier: 3.915A pdb=" N MET C 692 " --> pdb=" O TRP C 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 147 removed outlier: 3.882A pdb=" N LYS B 146 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 143 through 147' Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.652A pdb=" N THR B 187 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 327 through 339 removed outlier: 4.238A pdb=" N THR B 331 " --> pdb=" O GLY B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.909A pdb=" N SER B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 394 " --> pdb=" O MET B 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 389 through 394' Processing helix chain 'B' and resid 453 through 463 removed outlier: 4.079A pdb=" N GLN B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 removed outlier: 3.977A pdb=" N GLU B 483 " --> pdb=" O HIS B 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 480 through 483' Processing helix chain 'B' and resid 506 through 520 removed outlier: 3.640A pdb=" N CYS B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 removed outlier: 3.541A pdb=" N ASN B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 551 Processing helix chain 'B' and resid 553 through 578 Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 642 through 652 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.995A pdb=" N MET B 692 " --> pdb=" O TRP B 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'E' and resid 130 through 145 removed outlier: 3.579A pdb=" N TYR E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 98 through 112 Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 130 through 145 removed outlier: 3.583A pdb=" N TYR D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 439 removed outlier: 3.656A pdb=" N VAL F 436 " --> pdb=" O PHE F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 510 Processing helix chain 'F' and resid 526 through 530 removed outlier: 3.795A pdb=" N SER F 529 " --> pdb=" O ASP F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 Processing helix chain 'F' and resid 591 through 602 Processing helix chain 'F' and resid 610 through 619 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.614A pdb=" N TRP A 430 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL A 561 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG A 581 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 563 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 449 through 452 removed outlier: 6.983A pdb=" N HIS A 450 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 534 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 535 " --> pdb=" O GLY A 557 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY A 557 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG A 537 " --> pdb=" O TYR A 555 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR A 555 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 564 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 28 removed outlier: 4.197A pdb=" N VAL C 23 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY C 113 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 97 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 48 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TRP C 75 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 23 through 28 removed outlier: 4.197A pdb=" N VAL C 23 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU C 123 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 125 " --> pdb=" O ASN C 195 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 195 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N THR C 256 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 222 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 158 through 159 removed outlier: 6.598A pdb=" N LEU C 279 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS C 295 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 277 " --> pdb=" O LYS C 295 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR C 297 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 275 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL C 299 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 273 " --> pdb=" O VAL C 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 306 through 307 removed outlier: 8.286A pdb=" N MET C 401 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE C 376 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 342 through 346 removed outlier: 7.284A pdb=" N LEU C 315 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ALA C 344 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL C 317 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 346 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C 319 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 420 through 421 removed outlier: 6.393A pdb=" N VAL C 437 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU C 471 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 439 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 425 through 427 removed outlier: 3.565A pdb=" N VAL C 425 " --> pdb=" O TYR C 432 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 485 through 489 Processing sheet with id=AB3, first strand: chain 'C' and resid 591 through 594 Processing sheet with id=AB4, first strand: chain 'C' and resid 621 through 623 Processing sheet with id=AB5, first strand: chain 'C' and resid 636 through 637 Processing sheet with id=AB6, first strand: chain 'B' and resid 14 through 16 removed outlier: 7.448A pdb=" N ILE B 15 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 33 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 84 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 23 through 28 removed outlier: 4.283A pdb=" N VAL B 23 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 118 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 113 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B 97 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B 47 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 23 through 28 removed outlier: 4.283A pdb=" N VAL B 23 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 118 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 123 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER B 125 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 195 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR B 256 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL B 222 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 158 through 159 removed outlier: 6.620A pdb=" N LEU B 279 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 295 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 277 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR B 297 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR B 275 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 299 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 273 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 306 through 307 removed outlier: 8.331A pdb=" N MET B 401 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 376 " --> pdb=" O MET B 401 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 342 through 345 removed outlier: 7.261A pdb=" N LEU B 315 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N ALA B 344 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 317 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG B 681 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL B 317 " --> pdb=" O ASN B 679 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN B 679 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 419 through 421 removed outlier: 6.301A pdb=" N VAL B 437 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU B 471 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 439 " --> pdb=" O LEU B 471 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 425 through 427 removed outlier: 3.525A pdb=" N VAL B 425 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 485 through 489 Processing sheet with id=AC6, first strand: chain 'B' and resid 591 through 594 Processing sheet with id=AC7, first strand: chain 'B' and resid 621 through 623 Processing sheet with id=AC8, first strand: chain 'B' and resid 636 through 637 Processing sheet with id=AC9, first strand: chain 'E' and resid 23 through 26 removed outlier: 3.766A pdb=" N GLY E 24 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 34 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 26 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 23 through 26 removed outlier: 3.766A pdb=" N GLY E 24 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 34 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL E 26 " --> pdb=" O HIS E 32 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS E 32 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 23 through 26 removed outlier: 3.845A pdb=" N GLY D 24 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 34 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 26 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N HIS D 32 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA D 35 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA D 68 " --> pdb=" O THR D 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 429 through 430 removed outlier: 3.627A pdb=" N TRP F 430 " --> pdb=" O ASN F 553 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL F 561 " --> pdb=" O ARG F 581 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG F 581 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 563 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 449 through 452 removed outlier: 6.985A pdb=" N HIS F 450 " --> pdb=" O TYR F 458 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG F 534 " --> pdb=" O TYR F 458 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 535 " --> pdb=" O GLY F 557 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY F 557 " --> pdb=" O VAL F 535 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG F 537 " --> pdb=" O TYR F 555 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR F 555 " --> pdb=" O ARG F 537 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 564 " --> pdb=" O ALA F 522 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1416 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: 2.63 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4536 1.33 - 1.45: 2660 1.45 - 1.57: 9342 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 16678 Sorted by residual: bond pdb=" N ILE F 424 " pdb=" CA ILE F 424 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.60e-03 1.35e+04 2.20e+01 bond pdb=" N ILE A 424 " pdb=" CA ILE A 424 " ideal model delta sigma weight residual 1.460 1.493 -0.033 9.30e-03 1.16e+04 1.29e+01 bond pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.56e+00 bond pdb=" N VAL F 426 " pdb=" CA VAL F 426 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.33e+00 bond pdb=" N GLY A 423 " pdb=" CA GLY A 423 " ideal model delta sigma weight residual 1.446 1.475 -0.029 1.53e-02 4.27e+03 3.67e+00 ... (remaining 16673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 22200 1.71 - 3.42: 387 3.42 - 5.14: 48 5.14 - 6.85: 8 6.85 - 8.56: 5 Bond angle restraints: 22648 Sorted by residual: angle pdb=" C GLY A 423 " pdb=" N ILE A 424 " pdb=" CA ILE A 424 " ideal model delta sigma weight residual 123.46 117.66 5.80 1.60e+00 3.91e-01 1.31e+01 angle pdb=" CA ILE F 424 " pdb=" C ILE F 424 " pdb=" O ILE F 424 " ideal model delta sigma weight residual 120.88 118.52 2.36 6.80e-01 2.16e+00 1.20e+01 angle pdb=" CA VAL A 426 " pdb=" C VAL A 426 " pdb=" O VAL A 426 " ideal model delta sigma weight residual 121.36 117.83 3.53 1.10e+00 8.26e-01 1.03e+01 angle pdb=" CA LYS C 497 " pdb=" CB LYS C 497 " pdb=" CG LYS C 497 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" CA PRO A 425 " pdb=" C PRO A 425 " pdb=" O PRO A 425 " ideal model delta sigma weight residual 122.12 118.19 3.93 1.24e+00 6.50e-01 1.00e+01 ... (remaining 22643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 9020 17.76 - 35.52: 761 35.52 - 53.28: 234 53.28 - 71.03: 48 71.03 - 88.79: 15 Dihedral angle restraints: 10078 sinusoidal: 4071 harmonic: 6007 Sorted by residual: dihedral pdb=" CA GLN C 326 " pdb=" C GLN C 326 " pdb=" N GLY C 327 " pdb=" CA GLY C 327 " ideal model delta harmonic sigma weight residual -180.00 -157.05 -22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA ASP C 458 " pdb=" CB ASP C 458 " pdb=" CG ASP C 458 " pdb=" OD1 ASP C 458 " ideal model delta sinusoidal sigma weight residual -30.00 -87.73 57.73 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA LEU C 325 " pdb=" C LEU C 325 " pdb=" N GLN C 326 " pdb=" CA GLN C 326 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 10075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1546 0.031 - 0.062: 595 0.062 - 0.093: 150 0.093 - 0.123: 171 0.123 - 0.154: 19 Chirality restraints: 2481 Sorted by residual: chirality pdb=" CA ILE A 424 " pdb=" N ILE A 424 " pdb=" C ILE A 424 " pdb=" CB ILE A 424 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CB VAL C 94 " pdb=" CA VAL C 94 " pdb=" CG1 VAL C 94 " pdb=" CG2 VAL C 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE C 599 " pdb=" N ILE C 599 " pdb=" C ILE C 599 " pdb=" CB ILE C 599 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2478 not shown) Planarity restraints: 2933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 388 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO C 389 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 389 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 389 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 388 " -0.048 5.00e-02 4.00e+02 7.28e-02 8.49e+00 pdb=" N PRO B 389 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 389 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 389 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 24 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO E 25 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO E 25 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 25 " 0.036 5.00e-02 4.00e+02 ... (remaining 2930 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2152 2.76 - 3.29: 14307 3.29 - 3.83: 24206 3.83 - 4.36: 27646 4.36 - 4.90: 50799 Nonbonded interactions: 119110 Sorted by model distance: nonbonded pdb=" N GLU A 609 " pdb=" OE1 GLU A 609 " model vdw 2.220 3.120 nonbonded pdb=" NE1 TRP B 224 " pdb=" OE1 GLU B 255 " model vdw 2.230 3.120 nonbonded pdb=" NE1 TRP C 224 " pdb=" OE1 GLU C 255 " model vdw 2.234 3.120 nonbonded pdb=" OG SER C 283 " pdb=" O ILE C 288 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG B 607 " pdb=" O SER B 608 " model vdw 2.262 3.120 ... (remaining 119105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = (chain 'C' and resid 11 through 694) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.720 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16678 Z= 0.139 Angle : 0.571 8.562 22648 Z= 0.309 Chirality : 0.043 0.154 2481 Planarity : 0.005 0.074 2933 Dihedral : 14.886 88.793 6216 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.72 % Allowed : 25.51 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.87 (0.18), residues: 2053 helix: 1.04 (0.26), residues: 413 sheet: 1.32 (0.24), residues: 521 loop : 0.12 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 528 TYR 0.011 0.001 TYR C 561 PHE 0.012 0.001 PHE C 614 TRP 0.013 0.001 TRP D 33 HIS 0.002 0.000 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00263 (16678) covalent geometry : angle 0.57075 (22648) hydrogen bonds : bond 0.21804 ( 517) hydrogen bonds : angle 7.38892 ( 1416) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.625 Fit side-chains REVERT: E 116 ASP cc_start: 0.6821 (p0) cc_final: 0.6026 (p0) REVERT: E 117 ASP cc_start: 0.7264 (t70) cc_final: 0.5999 (p0) outliers start: 13 outliers final: 12 residues processed: 207 average time/residue: 0.1228 time to fit residues: 37.6795 Evaluate side-chains 194 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ASP Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0020 overall best weight: 1.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 ASN C 324 GLN B 324 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.183000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139195 restraints weight = 21487.893| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.84 r_work: 0.3626 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16678 Z= 0.145 Angle : 0.583 8.465 22648 Z= 0.301 Chirality : 0.046 0.153 2481 Planarity : 0.005 0.064 2933 Dihedral : 4.297 44.751 2258 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.72 % Allowed : 22.29 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.80 (0.18), residues: 2053 helix: 1.15 (0.25), residues: 429 sheet: 1.17 (0.23), residues: 531 loop : 0.03 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 528 TYR 0.013 0.001 TYR B 667 PHE 0.016 0.001 PHE C 614 TRP 0.011 0.001 TRP E 33 HIS 0.004 0.001 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.00352 (16678) covalent geometry : angle 0.58331 (22648) hydrogen bonds : bond 0.05351 ( 517) hydrogen bonds : angle 5.35285 ( 1416) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.612 Fit side-chains REVERT: A 435 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: C 138 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7629 (mmm) REVERT: C 387 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: B 138 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7922 (mpp) REVERT: B 214 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7870 (mtpm) REVERT: B 290 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: B 448 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: E 143 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7081 (mm110) REVERT: F 551 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7428 (tt0) outliers start: 67 outliers final: 30 residues processed: 232 average time/residue: 0.1210 time to fit residues: 41.4992 Evaluate side-chains 208 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 551 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 43 optimal weight: 0.0010 chunk 134 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 158 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS B 324 GLN F 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.185333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142182 restraints weight = 21637.650| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.77 r_work: 0.3662 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16678 Z= 0.093 Angle : 0.500 6.288 22648 Z= 0.257 Chirality : 0.043 0.151 2481 Planarity : 0.004 0.057 2933 Dihedral : 3.748 58.844 2240 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.06 % Allowed : 22.35 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.92 (0.18), residues: 2053 helix: 1.37 (0.26), residues: 429 sheet: 1.29 (0.23), residues: 514 loop : 0.04 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 554 TYR 0.008 0.001 TYR E 134 PHE 0.010 0.001 PHE C 614 TRP 0.008 0.001 TRP E 33 HIS 0.002 0.000 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00204 (16678) covalent geometry : angle 0.50035 (22648) hydrogen bonds : bond 0.04161 ( 517) hydrogen bonds : angle 4.87192 ( 1416) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: C 138 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7605 (mmm) REVERT: C 159 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8440 (tp) REVERT: C 330 ASP cc_start: 0.7826 (m-30) cc_final: 0.7494 (t0) REVERT: B 214 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7885 (mtpm) REVERT: B 515 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7347 (ttm170) REVERT: B 673 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: E 143 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.7104 (mm110) REVERT: D 29 ASP cc_start: 0.6587 (t0) cc_final: 0.6265 (t0) REVERT: F 551 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7373 (tt0) outliers start: 55 outliers final: 32 residues processed: 223 average time/residue: 0.1245 time to fit residues: 41.6155 Evaluate side-chains 215 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 515 ARG Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 551 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 133 optimal weight: 0.3980 chunk 194 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 155 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS C 567 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.185502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.141959 restraints weight = 21604.310| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.83 r_work: 0.3661 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16678 Z= 0.092 Angle : 0.493 6.590 22648 Z= 0.251 Chirality : 0.043 0.144 2481 Planarity : 0.004 0.052 2933 Dihedral : 3.546 47.136 2238 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.61 % Allowed : 21.85 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.96 (0.18), residues: 2053 helix: 1.47 (0.26), residues: 429 sheet: 1.27 (0.23), residues: 514 loop : 0.07 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 321 TYR 0.007 0.001 TYR E 134 PHE 0.011 0.001 PHE C 614 TRP 0.006 0.001 TRP C 224 HIS 0.002 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00209 (16678) covalent geometry : angle 0.49278 (22648) hydrogen bonds : bond 0.03767 ( 517) hydrogen bonds : angle 4.61192 ( 1416) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 183 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: A 546 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6899 (pptt) REVERT: C 138 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7613 (mmm) REVERT: C 159 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8453 (tp) REVERT: C 330 ASP cc_start: 0.7902 (m-30) cc_final: 0.7596 (t0) REVERT: C 387 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7811 (pm20) REVERT: B 138 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7887 (mpp) REVERT: B 342 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7866 (mm-40) REVERT: B 448 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7248 (mt-10) REVERT: B 452 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8747 (ttp) REVERT: B 654 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8030 (mp) REVERT: B 673 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: E 143 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7120 (mm110) REVERT: D 29 ASP cc_start: 0.6258 (t0) cc_final: 0.5885 (t0) REVERT: F 546 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6896 (pptt) REVERT: F 551 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7304 (tt0) outliers start: 65 outliers final: 37 residues processed: 228 average time/residue: 0.1226 time to fit residues: 41.1906 Evaluate side-chains 226 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 620 MET Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 546 LYS Chi-restraints excluded: chain F residue 551 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 54 optimal weight: 0.0770 chunk 96 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141273 restraints weight = 21394.403| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.87 r_work: 0.3647 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16678 Z= 0.096 Angle : 0.492 6.080 22648 Z= 0.251 Chirality : 0.043 0.148 2481 Planarity : 0.004 0.049 2933 Dihedral : 3.481 35.321 2236 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.11 % Allowed : 20.96 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.98 (0.18), residues: 2053 helix: 1.50 (0.26), residues: 429 sheet: 1.28 (0.23), residues: 512 loop : 0.07 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 321 TYR 0.008 0.001 TYR E 134 PHE 0.012 0.001 PHE C 614 TRP 0.006 0.001 TRP C 224 HIS 0.002 0.001 HIS C 567 Details of bonding type rmsd covalent geometry : bond 0.00222 (16678) covalent geometry : angle 0.49224 (22648) hydrogen bonds : bond 0.03790 ( 517) hydrogen bonds : angle 4.48026 ( 1416) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 189 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: A 546 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6771 (pptt) REVERT: C 138 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7634 (mmm) REVERT: C 159 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8444 (tp) REVERT: C 330 ASP cc_start: 0.7928 (m-30) cc_final: 0.7688 (t0) REVERT: C 387 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: B 138 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7989 (mpp) REVERT: B 342 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7988 (mm-40) REVERT: B 387 GLU cc_start: 0.8272 (pm20) cc_final: 0.8064 (pm20) REVERT: B 448 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: B 452 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8865 (ttp) REVERT: B 654 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7987 (mp) REVERT: B 673 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: E 143 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7174 (mm110) REVERT: D 29 ASP cc_start: 0.6057 (t0) cc_final: 0.5671 (t0) REVERT: F 551 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7423 (tt0) outliers start: 74 outliers final: 42 residues processed: 243 average time/residue: 0.1298 time to fit residues: 46.3061 Evaluate side-chains 235 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 148 TRP Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 551 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS B 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135622 restraints weight = 21420.589| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.84 r_work: 0.3578 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16678 Z= 0.169 Angle : 0.589 6.459 22648 Z= 0.305 Chirality : 0.047 0.151 2481 Planarity : 0.005 0.050 2933 Dihedral : 3.955 29.719 2236 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.95 % Allowed : 20.96 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.18), residues: 2053 helix: 1.29 (0.25), residues: 429 sheet: 1.03 (0.23), residues: 526 loop : -0.15 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 321 TYR 0.014 0.002 TYR C 444 PHE 0.019 0.002 PHE C 614 TRP 0.009 0.001 TRP D 33 HIS 0.004 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00422 (16678) covalent geometry : angle 0.58861 (22648) hydrogen bonds : bond 0.05306 ( 517) hydrogen bonds : angle 4.72402 ( 1416) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: A 546 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7069 (pptt) REVERT: C 123 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8057 (pp20) REVERT: C 138 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7688 (mmm) REVERT: C 330 ASP cc_start: 0.8010 (m-30) cc_final: 0.7748 (t0) REVERT: C 342 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7906 (mm-40) REVERT: C 387 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: B 138 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7948 (mpp) REVERT: B 324 GLN cc_start: 0.7354 (tt0) cc_final: 0.7042 (tt0) REVERT: B 342 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7907 (mm-40) REVERT: B 414 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8790 (t0) REVERT: B 448 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 670 GLU cc_start: 0.7293 (pm20) cc_final: 0.6960 (pm20) REVERT: B 673 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: E 143 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7253 (mm110) REVERT: D 29 ASP cc_start: 0.6056 (t0) cc_final: 0.5679 (t0) REVERT: F 546 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7007 (pptt) outliers start: 71 outliers final: 43 residues processed: 233 average time/residue: 0.1177 time to fit residues: 40.5386 Evaluate side-chains 219 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 435 GLN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 546 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 85 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN C 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135774 restraints weight = 21405.155| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.83 r_work: 0.3576 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16678 Z= 0.153 Angle : 0.567 5.763 22648 Z= 0.295 Chirality : 0.046 0.147 2481 Planarity : 0.005 0.051 2933 Dihedral : 4.044 33.459 2236 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.61 % Allowed : 21.51 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.48 (0.18), residues: 2053 helix: 1.14 (0.25), residues: 429 sheet: 0.94 (0.23), residues: 524 loop : -0.27 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 570 TYR 0.010 0.001 TYR C 444 PHE 0.018 0.001 PHE B 443 TRP 0.011 0.001 TRP E 33 HIS 0.003 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00379 (16678) covalent geometry : angle 0.56670 (22648) hydrogen bonds : bond 0.05050 ( 517) hydrogen bonds : angle 4.75563 ( 1416) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7042 (pptt) REVERT: C 123 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: C 138 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7661 (mmm) REVERT: C 330 ASP cc_start: 0.7969 (m-30) cc_final: 0.7720 (t0) REVERT: C 342 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7900 (mm-40) REVERT: C 387 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: C 623 MET cc_start: 0.8885 (mmm) cc_final: 0.8496 (mmm) REVERT: B 138 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: B 324 GLN cc_start: 0.7311 (tt0) cc_final: 0.6957 (tt0) REVERT: B 342 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7929 (mm-40) REVERT: B 414 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8810 (t0) REVERT: B 448 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 670 GLU cc_start: 0.7449 (pm20) cc_final: 0.7139 (pm20) REVERT: B 673 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: E 143 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7240 (mm110) REVERT: D 29 ASP cc_start: 0.5979 (t0) cc_final: 0.5612 (t0) REVERT: F 546 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7009 (pptt) outliers start: 65 outliers final: 43 residues processed: 216 average time/residue: 0.1139 time to fit residues: 36.1107 Evaluate side-chains 223 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 546 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 5 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 GLN C 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.174900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132918 restraints weight = 21129.952| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.62 r_work: 0.3543 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16678 Z= 0.202 Angle : 0.649 7.262 22648 Z= 0.338 Chirality : 0.049 0.163 2481 Planarity : 0.005 0.051 2933 Dihedral : 4.550 50.404 2235 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.72 % Allowed : 21.68 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.13 (0.18), residues: 2053 helix: 1.00 (0.25), residues: 427 sheet: 0.62 (0.22), residues: 524 loop : -0.51 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 321 TYR 0.012 0.002 TYR B 400 PHE 0.030 0.002 PHE B 443 TRP 0.011 0.002 TRP B 224 HIS 0.005 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00507 (16678) covalent geometry : angle 0.64907 (22648) hydrogen bonds : bond 0.06098 ( 517) hydrogen bonds : angle 5.00723 ( 1416) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7192 (pptt) REVERT: C 123 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7826 (pp20) REVERT: C 138 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7745 (mmm) REVERT: C 330 ASP cc_start: 0.7908 (m-30) cc_final: 0.7581 (t0) REVERT: C 342 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7949 (mm-40) REVERT: C 387 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: C 420 MET cc_start: 0.8687 (ttt) cc_final: 0.8331 (ttt) REVERT: C 623 MET cc_start: 0.8987 (mmm) cc_final: 0.8625 (mmm) REVERT: B 138 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7862 (mpp) REVERT: B 221 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8735 (ttp-170) REVERT: B 342 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7897 (mm-40) REVERT: B 414 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8807 (t0) REVERT: B 448 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: B 670 GLU cc_start: 0.7562 (pm20) cc_final: 0.7280 (pm20) REVERT: B 673 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: E 143 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7199 (mm110) REVERT: D 29 ASP cc_start: 0.5958 (t0) cc_final: 0.5663 (t0) outliers start: 67 outliers final: 48 residues processed: 232 average time/residue: 0.1121 time to fit residues: 38.0925 Evaluate side-chains 231 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 570 ARG Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 221 ARG Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 87 ASP Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 459 SER Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 43 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 191 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 GLN C 252 HIS B 567 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.180346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137081 restraints weight = 21359.659| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.74 r_work: 0.3603 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16678 Z= 0.106 Angle : 0.528 10.186 22648 Z= 0.274 Chirality : 0.044 0.148 2481 Planarity : 0.004 0.051 2933 Dihedral : 4.103 48.037 2235 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.56 % Allowed : 22.90 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.18), residues: 2053 helix: 1.16 (0.25), residues: 428 sheet: 0.84 (0.22), residues: 529 loop : -0.33 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 570 TYR 0.010 0.001 TYR E 134 PHE 0.015 0.001 PHE B 443 TRP 0.009 0.001 TRP B 224 HIS 0.005 0.001 HIS B 567 Details of bonding type rmsd covalent geometry : bond 0.00248 (16678) covalent geometry : angle 0.52842 (22648) hydrogen bonds : bond 0.04203 ( 517) hydrogen bonds : angle 4.72184 ( 1416) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7709 (mmm) REVERT: C 330 ASP cc_start: 0.7951 (m-30) cc_final: 0.7702 (t0) REVERT: C 387 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: C 623 MET cc_start: 0.8922 (mmm) cc_final: 0.8588 (mmm) REVERT: B 221 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8714 (ttp-170) REVERT: B 324 GLN cc_start: 0.7080 (tt0) cc_final: 0.6798 (tt0) REVERT: B 342 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: B 448 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: B 673 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: E 143 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7244 (mm110) REVERT: D 29 ASP cc_start: 0.5877 (t0) cc_final: 0.5585 (t0) REVERT: D 46 GLN cc_start: 0.7734 (mt0) cc_final: 0.7330 (mm-40) outliers start: 46 outliers final: 32 residues processed: 207 average time/residue: 0.1298 time to fit residues: 39.1767 Evaluate side-chains 211 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 221 ARG Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ASP Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 516 ILE Chi-restraints excluded: chain F residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 0.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.182486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139807 restraints weight = 21280.586| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.70 r_work: 0.3637 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16678 Z= 0.092 Angle : 0.500 6.072 22648 Z= 0.257 Chirality : 0.043 0.153 2481 Planarity : 0.004 0.049 2933 Dihedral : 3.738 42.969 2235 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.89 % Allowed : 23.57 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.65 (0.18), residues: 2053 helix: 1.33 (0.26), residues: 429 sheet: 0.97 (0.22), residues: 535 loop : -0.16 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 570 TYR 0.008 0.001 TYR B 365 PHE 0.013 0.001 PHE B 443 TRP 0.008 0.001 TRP B 150 HIS 0.002 0.000 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00208 (16678) covalent geometry : angle 0.49969 (22648) hydrogen bonds : bond 0.03476 ( 517) hydrogen bonds : angle 4.47591 ( 1416) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4106 Ramachandran restraints generated. 2053 Oldfield, 0 Emsley, 2053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8307 (mt0) cc_final: 0.8049 (mt0) REVERT: C 330 ASP cc_start: 0.7909 (m-30) cc_final: 0.7688 (t0) REVERT: C 387 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7797 (pm20) REVERT: C 623 MET cc_start: 0.8834 (mmm) cc_final: 0.8547 (mmm) REVERT: B 221 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8652 (ttp-170) REVERT: B 324 GLN cc_start: 0.6921 (tt0) cc_final: 0.6614 (tt0) REVERT: B 342 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7889 (mm-40) REVERT: B 448 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: B 670 GLU cc_start: 0.7191 (pm20) cc_final: 0.6900 (pm20) REVERT: B 673 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: E 29 ASP cc_start: 0.6155 (t0) cc_final: 0.5751 (t0) REVERT: E 143 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7232 (mm110) REVERT: D 29 ASP cc_start: 0.5774 (t0) cc_final: 0.5496 (t0) REVERT: D 46 GLN cc_start: 0.7702 (mt0) cc_final: 0.7354 (mm-40) REVERT: F 599 LYS cc_start: 0.7003 (mtpp) cc_final: 0.6786 (mmmt) outliers start: 34 outliers final: 24 residues processed: 214 average time/residue: 0.1171 time to fit residues: 37.2515 Evaluate side-chains 210 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 546 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 221 ARG Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 546 ILE Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 516 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 182 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 26 optimal weight: 0.0060 chunk 164 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS E 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.180884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138126 restraints weight = 21351.279| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.70 r_work: 0.3615 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16678 Z= 0.109 Angle : 0.519 7.422 22648 Z= 0.267 Chirality : 0.044 0.147 2481 Planarity : 0.004 0.049 2933 Dihedral : 3.802 43.324 2235 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.33 % Allowed : 22.79 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.62 (0.18), residues: 2053 helix: 1.31 (0.26), residues: 427 sheet: 0.94 (0.22), residues: 530 loop : -0.17 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 554 TYR 0.009 0.001 TYR B 365 PHE 0.017 0.001 PHE C 443 TRP 0.007 0.001 TRP B 224 HIS 0.003 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00258 (16678) covalent geometry : angle 0.51911 (22648) hydrogen bonds : bond 0.03918 ( 517) hydrogen bonds : angle 4.48641 ( 1416) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4610.66 seconds wall clock time: 79 minutes 22.44 seconds (4762.44 seconds total)