Starting phenix.real_space_refine on Thu Sep 18 19:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3y_44160/09_2025/9b3y_44160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3y_44160/09_2025/9b3y_44160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3y_44160/09_2025/9b3y_44160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3y_44160/09_2025/9b3y_44160.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3y_44160/09_2025/9b3y_44160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3y_44160/09_2025/9b3y_44160.cif" } resolution = 2.7 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= 0.004 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 116 5.16 5 C 12952 2.51 5 N 3292 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19744 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4882 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 587} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PEX': 1, 'RTO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.02, per 1000 atoms: 0.20 Number of scatterers: 19744 At special positions: 0 Unit cell: (136.95, 136.95, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 P 4 15.00 O 3380 8.00 N 3292 7.00 C 12952 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: 1.67 Conformation dependent library (CDL) restraints added in 923.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4584 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 65.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.538A pdb=" N ARG A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.578A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.537A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 320 through 327 removed outlier: 4.164A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 412 removed outlier: 5.307A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 3.651A pdb=" N ILE A 463 " --> pdb=" O ARG A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.627A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.716A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.676A pdb=" N VAL A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A 530 " --> pdb=" O SER A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 3.858A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.790A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 717 removed outlier: 4.151A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.538A pdb=" N ARG B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.578A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.537A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.164A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Proline residue: B 325 - end of helix Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 377 through 412 removed outlier: 5.307A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 460 through 463 removed outlier: 3.651A pdb=" N ILE B 463 " --> pdb=" O ARG B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.627A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.716A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 519 through 530 removed outlier: 3.676A pdb=" N VAL B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 530 " --> pdb=" O SER B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 3.858A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.790A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 717 removed outlier: 4.151A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.538A pdb=" N ARG C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 135 through 147 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.578A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.537A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 320 through 327 removed outlier: 4.164A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 412 removed outlier: 5.307A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 460 through 463 removed outlier: 3.651A pdb=" N ILE C 463 " --> pdb=" O ARG C 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 463' Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.627A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.716A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 519 through 530 removed outlier: 3.676A pdb=" N VAL C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 530 " --> pdb=" O SER C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 3.858A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 603 removed outlier: 3.790A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 717 removed outlier: 4.151A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.537A pdb=" N ARG D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 135 through 147 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.578A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.537A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.164A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Proline residue: D 325 - end of helix Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 412 removed outlier: 5.307A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 460 through 463 removed outlier: 3.651A pdb=" N ILE D 463 " --> pdb=" O ARG D 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 460 through 463' Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.627A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.716A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 519 through 530 removed outlier: 3.676A pdb=" N VAL D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN D 530 " --> pdb=" O SER D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 3.858A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 603 removed outlier: 3.790A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 717 removed outlier: 4.151A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.708A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP A 700 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AA3, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.708A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP B 700 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 674 through 675 Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.709A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP C 700 " --> pdb=" O VAL C 691 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 674 through 675 Processing sheet with id=AA7, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.709A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP D 700 " --> pdb=" O VAL D 691 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 674 through 675 1108 hydrogen bonds defined for protein. 3168 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: 2.96 Time building geometry restraints manager: 2.22 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: 4588 1.33 - 1.45: 4245 1.45 - 1.58: 11199 1.58 - 1.70: 12 1.70 - 1.82: 176 Bond restraints: 20220 Sorted by residual: bond pdb=" C PHE D 75 " pdb=" N ASP D 76 " ideal model delta sigma weight residual 1.331 1.253 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" C PHE A 75 " pdb=" N ASP A 76 " ideal model delta sigma weight residual 1.331 1.253 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" C PHE C 75 " pdb=" N ASP C 76 " ideal model delta sigma weight residual 1.331 1.253 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" C PHE B 75 " pdb=" N ASP B 76 " ideal model delta sigma weight residual 1.331 1.253 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" C17 RTO D 802 " pdb=" O19 RTO D 802 " ideal model delta sigma weight residual 1.256 1.343 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 20215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 18790 1.74 - 3.49: 7203 3.49 - 5.23: 1225 5.23 - 6.98: 170 6.98 - 8.72: 16 Bond angle restraints: 27404 Sorted by residual: angle pdb=" CA ASP A 243 " pdb=" CB ASP A 243 " pdb=" CG ASP A 243 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA ASP B 243 " pdb=" CB ASP B 243 " pdb=" CG ASP B 243 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA ASP C 243 " pdb=" CB ASP C 243 " pdb=" CG ASP C 243 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA ASP D 243 " pdb=" CB ASP D 243 " pdb=" CG ASP D 243 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA PHE D 547 " pdb=" CB PHE D 547 " pdb=" CG PHE D 547 " ideal model delta sigma weight residual 113.80 119.14 -5.34 1.00e+00 1.00e+00 2.85e+01 ... (remaining 27399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 11081 17.69 - 35.37: 635 35.37 - 53.06: 144 53.06 - 70.75: 60 70.75 - 88.43: 24 Dihedral angle restraints: 11944 sinusoidal: 4852 harmonic: 7092 Sorted by residual: dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE A 209 " pdb=" C PHE A 209 " pdb=" N GLY A 210 " pdb=" CA GLY A 210 " ideal model delta harmonic sigma weight residual 180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE C 209 " pdb=" C PHE C 209 " pdb=" N GLY C 210 " pdb=" CA GLY C 210 " ideal model delta harmonic sigma weight residual 180.00 -151.01 -28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 11941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2010 0.081 - 0.161: 922 0.161 - 0.242: 123 0.242 - 0.322: 41 0.322 - 0.403: 4 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA GLU B 231 " pdb=" N GLU B 231 " pdb=" C GLU B 231 " pdb=" CB GLU B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA GLU D 231 " pdb=" N GLU D 231 " pdb=" C GLU D 231 " pdb=" CB GLU D 231 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA GLU C 231 " pdb=" N GLU C 231 " pdb=" C GLU C 231 " pdb=" CB GLU C 231 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 3097 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 509 " -0.108 2.00e-02 2.50e+03 5.68e-02 8.06e+01 pdb=" CG TRP B 509 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP B 509 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 509 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP B 509 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP B 509 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 509 " 0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 509 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 509 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP B 509 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 509 " -0.108 2.00e-02 2.50e+03 5.68e-02 8.06e+01 pdb=" CG TRP A 509 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP A 509 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP A 509 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A 509 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP A 509 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 509 " 0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 509 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 509 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 509 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 509 " 0.108 2.00e-02 2.50e+03 5.68e-02 8.06e+01 pdb=" CG TRP C 509 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP C 509 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP C 509 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP C 509 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TRP C 509 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 509 " -0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 509 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 509 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP C 509 " 0.064 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 8627 2.98 - 3.46: 19992 3.46 - 3.94: 34488 3.94 - 4.42: 37563 4.42 - 4.90: 63684 Nonbonded interactions: 164354 Sorted by model distance: nonbonded pdb=" NH2 ARG B 388 " pdb=" OE1 GLU B 685 " model vdw 2.499 3.120 nonbonded pdb=" NH2 ARG A 388 " pdb=" OE1 GLU A 685 " model vdw 2.499 3.120 nonbonded pdb=" NH2 ARG C 388 " pdb=" OE1 GLU C 685 " model vdw 2.499 3.120 nonbonded pdb=" NH2 ARG D 388 " pdb=" OE1 GLU D 685 " model vdw 2.499 3.120 nonbonded pdb=" OG SER C 350 " pdb=" OE1 GLU C 672 " model vdw 2.520 3.040 ... (remaining 164349 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.012 0.087 20220 Z= 0.751 Angle : 1.792 8.724 27404 Z= 1.213 Chirality : 0.088 0.403 3100 Planarity : 0.013 0.093 3348 Dihedral : 13.703 88.433 7360 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.19 % Allowed : 0.95 % Favored : 98.85 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: -1.19 (0.15), residues: 2392 helix: -0.99 (0.11), residues: 1476 sheet: -0.03 (0.54), residues: 84 loop : -0.10 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 317 TYR 0.111 0.021 TYR A 447 PHE 0.058 0.011 PHE D 467 TRP 0.108 0.019 TRP A 509 HIS 0.010 0.003 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.01225 (20220) covalent geometry : angle 1.79154 (27404) hydrogen bonds : bond 0.15941 ( 1108) hydrogen bonds : angle 6.72771 ( 3168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 387 time to evaluate : 0.590 Fit side-chains REVERT: A 91 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7004 (mp0) REVERT: A 161 PHE cc_start: 0.7330 (m-80) cc_final: 0.6427 (m-80) REVERT: A 197 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7687 (tpt-90) REVERT: A 221 LYS cc_start: 0.7591 (mttm) cc_final: 0.7302 (mmtp) REVERT: A 240 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7108 (mp0) REVERT: A 339 ARG cc_start: 0.7971 (mtp85) cc_final: 0.7479 (mtp-110) REVERT: A 372 MET cc_start: 0.8838 (mtm) cc_final: 0.8633 (mtm) REVERT: A 433 MET cc_start: 0.6896 (mmm) cc_final: 0.6692 (mmp) REVERT: A 470 SER cc_start: 0.7918 (m) cc_final: 0.7649 (p) REVERT: A 530 GLN cc_start: 0.6403 (pt0) cc_final: 0.5038 (tp-100) REVERT: A 595 ASP cc_start: 0.5612 (m-30) cc_final: 0.5158 (t0) REVERT: A 645 MET cc_start: 0.8022 (mtt) cc_final: 0.7762 (mtp) REVERT: A 656 SER cc_start: 0.7838 (p) cc_final: 0.7290 (m) REVERT: A 679 ARG cc_start: 0.7015 (mtt180) cc_final: 0.6338 (mtm110) REVERT: A 687 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6806 (mtm-85) REVERT: B 91 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7003 (mp0) REVERT: B 161 PHE cc_start: 0.7330 (m-80) cc_final: 0.6425 (m-80) REVERT: B 197 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7686 (tpt-90) REVERT: B 221 LYS cc_start: 0.7590 (mttm) cc_final: 0.7306 (mmtp) REVERT: B 240 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7110 (mp0) REVERT: B 339 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7479 (mtp-110) REVERT: B 372 MET cc_start: 0.8838 (mtm) cc_final: 0.8633 (mtm) REVERT: B 433 MET cc_start: 0.6895 (mmm) cc_final: 0.6691 (mmp) REVERT: B 470 SER cc_start: 0.7916 (m) cc_final: 0.7647 (p) REVERT: B 530 GLN cc_start: 0.6402 (pt0) cc_final: 0.5037 (tp-100) REVERT: B 595 ASP cc_start: 0.5664 (m-30) cc_final: 0.5223 (t0) REVERT: B 645 MET cc_start: 0.8022 (mtt) cc_final: 0.7764 (mtp) REVERT: B 656 SER cc_start: 0.7837 (p) cc_final: 0.7290 (m) REVERT: B 679 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6337 (mtm110) REVERT: B 687 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6806 (mtm-85) REVERT: C 91 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7004 (mp0) REVERT: C 161 PHE cc_start: 0.7332 (m-80) cc_final: 0.6428 (m-80) REVERT: C 197 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7688 (tpt-90) REVERT: C 221 LYS cc_start: 0.7591 (mttm) cc_final: 0.7306 (mmtp) REVERT: C 240 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7108 (mp0) REVERT: C 339 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7479 (mtp-110) REVERT: C 372 MET cc_start: 0.8837 (mtm) cc_final: 0.8633 (mtm) REVERT: C 433 MET cc_start: 0.6896 (mmm) cc_final: 0.6693 (mmp) REVERT: C 470 SER cc_start: 0.7917 (m) cc_final: 0.7648 (p) REVERT: C 530 GLN cc_start: 0.6401 (pt0) cc_final: 0.5037 (tp-100) REVERT: C 595 ASP cc_start: 0.5666 (m-30) cc_final: 0.5224 (t0) REVERT: C 645 MET cc_start: 0.8023 (mtt) cc_final: 0.7764 (mtp) REVERT: C 656 SER cc_start: 0.7840 (p) cc_final: 0.7293 (m) REVERT: C 679 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6336 (mtm110) REVERT: C 687 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6807 (mtm-85) REVERT: D 91 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7003 (mp0) REVERT: D 161 PHE cc_start: 0.7331 (m-80) cc_final: 0.6428 (m-80) REVERT: D 197 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7687 (tpt-90) REVERT: D 221 LYS cc_start: 0.7591 (mttm) cc_final: 0.7307 (mmtp) REVERT: D 240 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7108 (mp0) REVERT: D 339 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7478 (mtp-110) REVERT: D 372 MET cc_start: 0.8837 (mtm) cc_final: 0.8632 (mtm) REVERT: D 433 MET cc_start: 0.6897 (mmm) cc_final: 0.6693 (mmp) REVERT: D 470 SER cc_start: 0.7918 (m) cc_final: 0.7648 (p) REVERT: D 530 GLN cc_start: 0.6402 (pt0) cc_final: 0.5037 (tp-100) REVERT: D 595 ASP cc_start: 0.5667 (m-30) cc_final: 0.5225 (t0) REVERT: D 645 MET cc_start: 0.8022 (mtt) cc_final: 0.7763 (mtp) REVERT: D 656 SER cc_start: 0.7840 (p) cc_final: 0.7293 (m) REVERT: D 679 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6337 (mtm110) REVERT: D 687 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6806 (mtm-85) outliers start: 4 outliers final: 0 residues processed: 391 average time/residue: 0.6224 time to fit residues: 272.4306 Evaluate side-chains 252 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 248 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain D residue 197 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123101 restraints weight = 22471.752| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.22 r_work: 0.3348 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20220 Z= 0.129 Angle : 0.541 5.794 27404 Z= 0.291 Chirality : 0.040 0.159 3100 Planarity : 0.004 0.041 3348 Dihedral : 9.680 76.703 2868 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.48 % Allowed : 6.73 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.08 (0.17), residues: 2392 helix: 1.09 (0.13), residues: 1496 sheet: 0.04 (0.49), residues: 116 loop : 0.32 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 280 TYR 0.017 0.001 TYR A 403 PHE 0.020 0.001 PHE B 467 TRP 0.022 0.002 TRP C 333 HIS 0.006 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00313 (20220) covalent geometry : angle 0.54098 (27404) hydrogen bonds : bond 0.03761 ( 1108) hydrogen bonds : angle 4.33024 ( 3168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.759 Fit side-chains REVERT: A 108 ASP cc_start: 0.6329 (m-30) cc_final: 0.5952 (p0) REVERT: A 151 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6656 (tt) REVERT: A 161 PHE cc_start: 0.6869 (m-80) cc_final: 0.6203 (m-80) REVERT: A 197 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7318 (tpt-90) REVERT: A 221 LYS cc_start: 0.7292 (mttm) cc_final: 0.6813 (mmtp) REVERT: A 240 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7666 (mt-10) REVERT: A 289 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7522 (mp0) REVERT: A 392 ARG cc_start: 0.6593 (ttt90) cc_final: 0.6212 (ttp-170) REVERT: A 530 GLN cc_start: 0.6246 (pt0) cc_final: 0.4787 (tp-100) REVERT: A 595 ASP cc_start: 0.5582 (m-30) cc_final: 0.5062 (t0) REVERT: A 645 MET cc_start: 0.7451 (mtt) cc_final: 0.7226 (mtp) REVERT: A 679 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6289 (mtm110) REVERT: A 687 ARG cc_start: 0.7500 (mtt180) cc_final: 0.6707 (mtm-85) REVERT: A 701 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7823 (mm-30) REVERT: B 108 ASP cc_start: 0.6337 (m-30) cc_final: 0.5955 (p0) REVERT: B 151 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6625 (tt) REVERT: B 161 PHE cc_start: 0.6874 (m-80) cc_final: 0.6207 (m-80) REVERT: B 197 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7315 (tpt-90) REVERT: B 221 LYS cc_start: 0.7303 (mttm) cc_final: 0.6831 (mmtp) REVERT: B 240 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 289 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7574 (mp0) REVERT: B 392 ARG cc_start: 0.6574 (ttt90) cc_final: 0.6195 (ttp-170) REVERT: B 530 GLN cc_start: 0.6258 (pt0) cc_final: 0.4805 (tp-100) REVERT: B 595 ASP cc_start: 0.5509 (m-30) cc_final: 0.4988 (t0) REVERT: B 645 MET cc_start: 0.7455 (mtt) cc_final: 0.7233 (mtp) REVERT: B 679 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6307 (mtm110) REVERT: B 687 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6671 (mtm-85) REVERT: B 701 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7838 (mm-30) REVERT: C 108 ASP cc_start: 0.6330 (m-30) cc_final: 0.5947 (p0) REVERT: C 151 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6615 (tt) REVERT: C 161 PHE cc_start: 0.6890 (m-80) cc_final: 0.6222 (m-80) REVERT: C 197 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7345 (tpt-90) REVERT: C 221 LYS cc_start: 0.7297 (mttm) cc_final: 0.6821 (mmtp) REVERT: C 240 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7646 (mt-10) REVERT: C 289 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7573 (mp0) REVERT: C 392 ARG cc_start: 0.6583 (ttt90) cc_final: 0.6201 (ttp-170) REVERT: C 530 GLN cc_start: 0.6256 (pt0) cc_final: 0.4798 (tp-100) REVERT: C 595 ASP cc_start: 0.5529 (m-30) cc_final: 0.5009 (t0) REVERT: C 645 MET cc_start: 0.7461 (mtt) cc_final: 0.7237 (mtp) REVERT: C 679 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6298 (mtm110) REVERT: C 687 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6786 (mtm-85) REVERT: C 701 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7837 (mm-30) REVERT: D 108 ASP cc_start: 0.6324 (m-30) cc_final: 0.5943 (p0) REVERT: D 151 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6604 (tt) REVERT: D 161 PHE cc_start: 0.6915 (m-80) cc_final: 0.6240 (m-80) REVERT: D 197 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7352 (tpt-90) REVERT: D 221 LYS cc_start: 0.7301 (mttm) cc_final: 0.6823 (mmtp) REVERT: D 240 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7643 (mt-10) REVERT: D 289 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7555 (mp0) REVERT: D 392 ARG cc_start: 0.6599 (ttt90) cc_final: 0.6223 (ttp-170) REVERT: D 530 GLN cc_start: 0.6259 (pt0) cc_final: 0.4797 (tp-100) REVERT: D 595 ASP cc_start: 0.5554 (m-30) cc_final: 0.5021 (t0) REVERT: D 645 MET cc_start: 0.7494 (mtt) cc_final: 0.7267 (mtp) REVERT: D 679 ARG cc_start: 0.7086 (mtt180) cc_final: 0.6304 (mtm110) REVERT: D 687 ARG cc_start: 0.7496 (mtt180) cc_final: 0.6767 (mtm-85) REVERT: D 701 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7825 (mm-30) outliers start: 31 outliers final: 0 residues processed: 320 average time/residue: 0.5953 time to fit residues: 214.9125 Evaluate side-chains 240 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 232 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 197 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 152 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 201 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 186 ASN C 186 ASN D 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.157271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.118616 restraints weight = 22949.763| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.26 r_work: 0.3281 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20220 Z= 0.195 Angle : 0.573 6.623 27404 Z= 0.297 Chirality : 0.041 0.175 3100 Planarity : 0.004 0.042 3348 Dihedral : 9.581 77.411 2868 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.72 % Allowed : 10.31 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.04 (0.17), residues: 2392 helix: 1.22 (0.13), residues: 1500 sheet: -0.41 (0.49), residues: 120 loop : -0.00 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 339 TYR 0.010 0.002 TYR B 403 PHE 0.015 0.002 PHE A 394 TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00491 (20220) covalent geometry : angle 0.57342 (27404) hydrogen bonds : bond 0.03776 ( 1108) hydrogen bonds : angle 4.29609 ( 3168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.763 Fit side-chains REVERT: A 161 PHE cc_start: 0.7010 (m-80) cc_final: 0.6524 (m-80) REVERT: A 221 LYS cc_start: 0.7334 (mttm) cc_final: 0.6923 (mmtp) REVERT: A 240 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 289 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7478 (mp0) REVERT: A 392 ARG cc_start: 0.6567 (ttt90) cc_final: 0.6127 (ttp-170) REVERT: A 530 GLN cc_start: 0.6101 (pt0) cc_final: 0.4741 (tp-100) REVERT: A 595 ASP cc_start: 0.5639 (m-30) cc_final: 0.4977 (t0) REVERT: A 609 GLU cc_start: 0.6759 (mt-10) cc_final: 0.5871 (tp30) REVERT: A 645 MET cc_start: 0.7522 (mtt) cc_final: 0.7264 (mtp) REVERT: A 679 ARG cc_start: 0.7157 (mtt180) cc_final: 0.6350 (mtm110) REVERT: A 687 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6613 (mtm-85) REVERT: A 690 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7827 (ttmt) REVERT: A 709 GLU cc_start: 0.7566 (tt0) cc_final: 0.6155 (mt-10) REVERT: B 161 PHE cc_start: 0.6999 (m-80) cc_final: 0.6507 (m-80) REVERT: B 221 LYS cc_start: 0.7329 (mttm) cc_final: 0.6914 (mmtp) REVERT: B 240 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 289 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7508 (mp0) REVERT: B 392 ARG cc_start: 0.6564 (ttt90) cc_final: 0.6123 (ttp-170) REVERT: B 530 GLN cc_start: 0.6119 (pt0) cc_final: 0.4760 (tp-100) REVERT: B 595 ASP cc_start: 0.5637 (m-30) cc_final: 0.4976 (t0) REVERT: B 609 GLU cc_start: 0.6747 (mt-10) cc_final: 0.5856 (tp30) REVERT: B 645 MET cc_start: 0.7505 (mtt) cc_final: 0.7245 (mtp) REVERT: B 679 ARG cc_start: 0.7166 (mtt180) cc_final: 0.6359 (mtm110) REVERT: B 687 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6606 (mtm-85) REVERT: B 690 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (ttmt) REVERT: B 709 GLU cc_start: 0.7542 (tt0) cc_final: 0.6137 (mt-10) REVERT: C 161 PHE cc_start: 0.6986 (m-80) cc_final: 0.6544 (m-80) REVERT: C 221 LYS cc_start: 0.7333 (mttm) cc_final: 0.6923 (mmtp) REVERT: C 240 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7694 (mt-10) REVERT: C 289 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7483 (mp0) REVERT: C 392 ARG cc_start: 0.6554 (ttt90) cc_final: 0.6111 (ttp-170) REVERT: C 530 GLN cc_start: 0.6101 (pt0) cc_final: 0.4739 (tp-100) REVERT: C 595 ASP cc_start: 0.5633 (m-30) cc_final: 0.4973 (t0) REVERT: C 609 GLU cc_start: 0.6756 (mt-10) cc_final: 0.5865 (tp30) REVERT: C 645 MET cc_start: 0.7513 (mtt) cc_final: 0.7258 (mtp) REVERT: C 679 ARG cc_start: 0.7154 (mtt180) cc_final: 0.6348 (mtm110) REVERT: C 687 ARG cc_start: 0.7380 (mtt180) cc_final: 0.6603 (mtm-85) REVERT: C 690 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7824 (ttmt) REVERT: C 709 GLU cc_start: 0.7550 (tt0) cc_final: 0.6142 (mt-10) REVERT: D 161 PHE cc_start: 0.7009 (m-80) cc_final: 0.6524 (m-80) REVERT: D 221 LYS cc_start: 0.7351 (mttm) cc_final: 0.6940 (mmtp) REVERT: D 240 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7700 (mt-10) REVERT: D 289 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7490 (mp0) REVERT: D 392 ARG cc_start: 0.6584 (ttt90) cc_final: 0.6138 (ttp-170) REVERT: D 530 GLN cc_start: 0.6104 (pt0) cc_final: 0.4740 (tp-100) REVERT: D 595 ASP cc_start: 0.5653 (m-30) cc_final: 0.4989 (t0) REVERT: D 609 GLU cc_start: 0.6751 (mt-10) cc_final: 0.5859 (tp30) REVERT: D 645 MET cc_start: 0.7532 (mtt) cc_final: 0.7267 (mtp) REVERT: D 679 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6365 (mtm110) REVERT: D 687 ARG cc_start: 0.7380 (mtt180) cc_final: 0.6611 (mtm-85) REVERT: D 690 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7819 (ttmt) REVERT: D 709 GLU cc_start: 0.7560 (tt0) cc_final: 0.6151 (mt-10) outliers start: 36 outliers final: 8 residues processed: 291 average time/residue: 0.5840 time to fit residues: 191.8159 Evaluate side-chains 252 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 690 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 134 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121838 restraints weight = 22844.038| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.27 r_work: 0.3323 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20220 Z= 0.107 Angle : 0.459 4.905 27404 Z= 0.244 Chirality : 0.038 0.139 3100 Planarity : 0.003 0.041 3348 Dihedral : 8.408 65.702 2852 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.10 % Allowed : 11.78 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.58 (0.17), residues: 2392 helix: 1.64 (0.13), residues: 1496 sheet: -0.25 (0.52), residues: 120 loop : 0.24 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 339 TYR 0.008 0.001 TYR A 525 PHE 0.013 0.001 PHE A 405 TRP 0.020 0.001 TRP D 333 HIS 0.003 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00252 (20220) covalent geometry : angle 0.45929 (27404) hydrogen bonds : bond 0.03069 ( 1108) hydrogen bonds : angle 4.02282 ( 3168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 260 time to evaluate : 0.762 Fit side-chains REVERT: A 161 PHE cc_start: 0.7001 (m-80) cc_final: 0.6607 (m-80) REVERT: A 221 LYS cc_start: 0.7283 (mttm) cc_final: 0.6893 (mmtp) REVERT: A 277 MET cc_start: 0.6484 (mtp) cc_final: 0.6272 (mtp) REVERT: A 289 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7493 (mp0) REVERT: A 309 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7574 (mm-30) REVERT: A 392 ARG cc_start: 0.6497 (ttt90) cc_final: 0.6067 (ttp-170) REVERT: A 530 GLN cc_start: 0.5913 (pt0) cc_final: 0.4755 (tp-100) REVERT: A 595 ASP cc_start: 0.5799 (m-30) cc_final: 0.5149 (t0) REVERT: A 609 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5623 (tp30) REVERT: A 645 MET cc_start: 0.7352 (mtt) cc_final: 0.7152 (mtp) REVERT: A 679 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6343 (mtm110) REVERT: A 687 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6763 (mtm-85) REVERT: A 690 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7812 (ttmt) REVERT: A 709 GLU cc_start: 0.7519 (tt0) cc_final: 0.6212 (mt-10) REVERT: B 161 PHE cc_start: 0.6981 (m-80) cc_final: 0.6581 (m-80) REVERT: B 221 LYS cc_start: 0.7293 (mttm) cc_final: 0.6894 (mmtp) REVERT: B 277 MET cc_start: 0.6460 (mtp) cc_final: 0.6248 (mtp) REVERT: B 289 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7504 (mp0) REVERT: B 309 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 392 ARG cc_start: 0.6527 (ttt90) cc_final: 0.6097 (ttp-170) REVERT: B 530 GLN cc_start: 0.5943 (pt0) cc_final: 0.4780 (tp-100) REVERT: B 595 ASP cc_start: 0.5765 (m-30) cc_final: 0.5119 (t0) REVERT: B 609 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5610 (tp30) REVERT: B 679 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6341 (mtm110) REVERT: B 687 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6745 (mtm-85) REVERT: B 690 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7797 (ttmt) REVERT: B 709 GLU cc_start: 0.7531 (tt0) cc_final: 0.6230 (mt-10) REVERT: C 161 PHE cc_start: 0.6993 (m-80) cc_final: 0.6583 (m-80) REVERT: C 221 LYS cc_start: 0.7291 (mttm) cc_final: 0.6902 (mmtp) REVERT: C 277 MET cc_start: 0.6511 (mtp) cc_final: 0.6298 (mtp) REVERT: C 289 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7503 (mp0) REVERT: C 309 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 392 ARG cc_start: 0.6479 (ttt90) cc_final: 0.6048 (ttp-170) REVERT: C 530 GLN cc_start: 0.5926 (pt0) cc_final: 0.4769 (tp-100) REVERT: C 595 ASP cc_start: 0.5747 (m-30) cc_final: 0.5104 (t0) REVERT: C 609 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5623 (tp30) REVERT: C 679 ARG cc_start: 0.7138 (mtt180) cc_final: 0.6319 (mtm110) REVERT: C 687 ARG cc_start: 0.7413 (mtt180) cc_final: 0.6735 (mtm-85) REVERT: C 690 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7802 (ttmt) REVERT: C 709 GLU cc_start: 0.7489 (tt0) cc_final: 0.6184 (mt-10) REVERT: D 161 PHE cc_start: 0.6986 (m-80) cc_final: 0.6593 (m-80) REVERT: D 221 LYS cc_start: 0.7309 (mttm) cc_final: 0.6919 (mmtp) REVERT: D 277 MET cc_start: 0.6509 (mtp) cc_final: 0.6295 (mtp) REVERT: D 289 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7500 (mp0) REVERT: D 309 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7595 (mm-30) REVERT: D 392 ARG cc_start: 0.6529 (ttt90) cc_final: 0.6095 (ttp-170) REVERT: D 530 GLN cc_start: 0.5940 (pt0) cc_final: 0.4777 (tp-100) REVERT: D 595 ASP cc_start: 0.5759 (m-30) cc_final: 0.5115 (t0) REVERT: D 609 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5606 (tp30) REVERT: D 679 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6344 (mtm110) REVERT: D 687 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6749 (mtm-85) REVERT: D 690 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7807 (ttmt) REVERT: D 709 GLU cc_start: 0.7510 (tt0) cc_final: 0.6200 (mt-10) outliers start: 44 outliers final: 12 residues processed: 280 average time/residue: 0.5900 time to fit residues: 186.9593 Evaluate side-chains 244 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 228 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 690 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 189 optimal weight: 0.3980 chunk 237 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122975 restraints weight = 22636.488| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.21 r_work: 0.3348 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20220 Z= 0.097 Angle : 0.439 6.635 27404 Z= 0.231 Chirality : 0.037 0.138 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.857 58.311 2852 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.10 % Allowed : 11.78 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.77 (0.17), residues: 2392 helix: 1.80 (0.13), residues: 1512 sheet: 0.52 (0.53), residues: 100 loop : 0.12 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.007 0.001 TYR D 525 PHE 0.014 0.001 PHE A 405 TRP 0.018 0.001 TRP D 333 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00224 (20220) covalent geometry : angle 0.43902 (27404) hydrogen bonds : bond 0.02851 ( 1108) hydrogen bonds : angle 3.87936 ( 3168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 269 time to evaluate : 0.732 Fit side-chains REVERT: A 161 PHE cc_start: 0.7038 (m-80) cc_final: 0.6706 (m-80) REVERT: A 193 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7994 (mtp85) REVERT: A 221 LYS cc_start: 0.7298 (mttm) cc_final: 0.6761 (mmtp) REVERT: A 289 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7499 (mp0) REVERT: A 309 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 392 ARG cc_start: 0.6610 (ttt90) cc_final: 0.6202 (ttp-170) REVERT: A 595 ASP cc_start: 0.5824 (m-30) cc_final: 0.5177 (t0) REVERT: A 679 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6339 (mtm110) REVERT: A 687 ARG cc_start: 0.7437 (mtt180) cc_final: 0.6821 (mtm-85) REVERT: A 690 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7611 (ttmt) REVERT: A 701 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7813 (mm-30) REVERT: A 709 GLU cc_start: 0.7444 (tt0) cc_final: 0.6201 (mt-10) REVERT: B 161 PHE cc_start: 0.7006 (m-80) cc_final: 0.6676 (m-80) REVERT: B 193 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7991 (mtp85) REVERT: B 221 LYS cc_start: 0.7270 (mttm) cc_final: 0.6726 (mmtp) REVERT: B 289 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7496 (mp0) REVERT: B 309 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7555 (mm-30) REVERT: B 392 ARG cc_start: 0.6611 (ttt90) cc_final: 0.6208 (ttp-170) REVERT: B 595 ASP cc_start: 0.5807 (m-30) cc_final: 0.5165 (t0) REVERT: B 679 ARG cc_start: 0.7031 (mtt180) cc_final: 0.6341 (mtm110) REVERT: B 687 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6809 (mtm-85) REVERT: B 690 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7601 (ttmt) REVERT: B 701 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7807 (mm-30) REVERT: B 709 GLU cc_start: 0.7442 (tt0) cc_final: 0.6200 (mt-10) REVERT: C 161 PHE cc_start: 0.7050 (m-80) cc_final: 0.6698 (m-80) REVERT: C 193 ARG cc_start: 0.8216 (mtp180) cc_final: 0.8001 (mtp85) REVERT: C 221 LYS cc_start: 0.7298 (mttm) cc_final: 0.6763 (mmtp) REVERT: C 289 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7518 (mp0) REVERT: C 309 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7547 (mm-30) REVERT: C 392 ARG cc_start: 0.6604 (ttt90) cc_final: 0.6195 (ttp-170) REVERT: C 595 ASP cc_start: 0.5795 (m-30) cc_final: 0.5150 (t0) REVERT: C 679 ARG cc_start: 0.7027 (mtt180) cc_final: 0.6328 (mtm110) REVERT: C 687 ARG cc_start: 0.7436 (mtt180) cc_final: 0.6818 (mtm-85) REVERT: C 690 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7622 (ttmt) REVERT: C 701 GLU cc_start: 0.8455 (mt-10) cc_final: 0.7829 (mm-30) REVERT: C 709 GLU cc_start: 0.7436 (tt0) cc_final: 0.6193 (mt-10) REVERT: D 161 PHE cc_start: 0.7015 (m-80) cc_final: 0.6690 (m-80) REVERT: D 193 ARG cc_start: 0.8199 (mtp180) cc_final: 0.7982 (mtp85) REVERT: D 221 LYS cc_start: 0.7302 (mttm) cc_final: 0.6767 (mmtp) REVERT: D 289 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7494 (mp0) REVERT: D 309 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7553 (mm-30) REVERT: D 392 ARG cc_start: 0.6618 (ttt90) cc_final: 0.6207 (ttp-170) REVERT: D 595 ASP cc_start: 0.5783 (m-30) cc_final: 0.5141 (t0) REVERT: D 679 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6353 (mtm110) REVERT: D 687 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6823 (mtm-85) REVERT: D 690 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7614 (ttmt) REVERT: D 701 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7827 (mm-30) REVERT: D 709 GLU cc_start: 0.7461 (tt0) cc_final: 0.6211 (mt-10) outliers start: 44 outliers final: 20 residues processed: 289 average time/residue: 0.5623 time to fit residues: 184.7449 Evaluate side-chains 257 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 690 LYS Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 690 LYS Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 690 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 197 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 62 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 6 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.161984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123455 restraints weight = 22721.589| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.22 r_work: 0.3355 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20220 Z= 0.092 Angle : 0.429 4.919 27404 Z= 0.226 Chirality : 0.037 0.130 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.756 58.910 2852 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.38 % Allowed : 12.26 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.89 (0.17), residues: 2392 helix: 1.91 (0.13), residues: 1512 sheet: 0.53 (0.52), residues: 100 loop : 0.15 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 339 TYR 0.006 0.001 TYR C 525 PHE 0.016 0.001 PHE A 405 TRP 0.021 0.001 TRP D 333 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00209 (20220) covalent geometry : angle 0.42923 (27404) hydrogen bonds : bond 0.02745 ( 1108) hydrogen bonds : angle 3.81282 ( 3168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.605 Fit side-chains REVERT: A 161 PHE cc_start: 0.6981 (m-80) cc_final: 0.6694 (m-80) REVERT: A 221 LYS cc_start: 0.7254 (mttm) cc_final: 0.6727 (mmtp) REVERT: A 289 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7468 (mp0) REVERT: A 309 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 392 ARG cc_start: 0.6601 (ttt90) cc_final: 0.6188 (ttp-170) REVERT: A 595 ASP cc_start: 0.5792 (m-30) cc_final: 0.5166 (t0) REVERT: A 613 GLN cc_start: 0.6514 (mm-40) cc_final: 0.5407 (mp10) REVERT: A 679 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6365 (mtm110) REVERT: A 687 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6814 (mtm-85) REVERT: A 701 GLU cc_start: 0.8452 (mt-10) cc_final: 0.7872 (mm-30) REVERT: A 709 GLU cc_start: 0.7436 (tt0) cc_final: 0.6217 (mt-10) REVERT: B 161 PHE cc_start: 0.6978 (m-80) cc_final: 0.6692 (m-80) REVERT: B 221 LYS cc_start: 0.7262 (mttm) cc_final: 0.6717 (mmtp) REVERT: B 289 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7489 (mp0) REVERT: B 309 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 392 ARG cc_start: 0.6598 (ttt90) cc_final: 0.6193 (ttp-170) REVERT: B 595 ASP cc_start: 0.5775 (m-30) cc_final: 0.5154 (t0) REVERT: B 613 GLN cc_start: 0.6530 (mm-40) cc_final: 0.5413 (mp10) REVERT: B 679 ARG cc_start: 0.7058 (mtt180) cc_final: 0.6376 (mtm110) REVERT: B 687 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6795 (mtm-85) REVERT: B 701 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7866 (mm-30) REVERT: B 709 GLU cc_start: 0.7422 (tt0) cc_final: 0.6203 (mt-10) REVERT: C 161 PHE cc_start: 0.7001 (m-80) cc_final: 0.6697 (m-80) REVERT: C 221 LYS cc_start: 0.7250 (mttm) cc_final: 0.6720 (mmtp) REVERT: C 289 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7504 (mp0) REVERT: C 309 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 392 ARG cc_start: 0.6584 (ttt90) cc_final: 0.6174 (ttp-170) REVERT: C 595 ASP cc_start: 0.5750 (m-30) cc_final: 0.5130 (t0) REVERT: C 613 GLN cc_start: 0.6527 (mm-40) cc_final: 0.5409 (mp10) REVERT: C 679 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6363 (mtm110) REVERT: C 687 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6802 (mtm-85) REVERT: C 701 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7889 (mm-30) REVERT: C 709 GLU cc_start: 0.7445 (tt0) cc_final: 0.6227 (mt-10) REVERT: D 161 PHE cc_start: 0.6982 (m-80) cc_final: 0.6689 (m-80) REVERT: D 221 LYS cc_start: 0.7244 (mttm) cc_final: 0.6715 (mmtp) REVERT: D 289 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7494 (mp0) REVERT: D 309 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7403 (mm-30) REVERT: D 392 ARG cc_start: 0.6609 (ttt90) cc_final: 0.6196 (ttp-170) REVERT: D 595 ASP cc_start: 0.5709 (m-30) cc_final: 0.5096 (t0) REVERT: D 613 GLN cc_start: 0.6527 (mm-40) cc_final: 0.5407 (mp10) REVERT: D 679 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6372 (mtm110) REVERT: D 687 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6803 (mtm-85) REVERT: D 701 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7902 (mm-30) REVERT: D 709 GLU cc_start: 0.7442 (tt0) cc_final: 0.6215 (mt-10) outliers start: 29 outliers final: 24 residues processed: 268 average time/residue: 0.5487 time to fit residues: 167.8789 Evaluate side-chains 271 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 247 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 534 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 157 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 chunk 234 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121919 restraints weight = 22781.226| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.28 r_work: 0.3356 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20220 Z= 0.102 Angle : 0.447 8.527 27404 Z= 0.231 Chirality : 0.037 0.124 3100 Planarity : 0.003 0.041 3348 Dihedral : 7.754 59.543 2852 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.96 % Allowed : 11.83 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.91 (0.17), residues: 2392 helix: 1.99 (0.13), residues: 1484 sheet: 0.55 (0.52), residues: 100 loop : 0.07 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.011 0.001 TYR A 228 PHE 0.018 0.001 PHE C 405 TRP 0.025 0.001 TRP D 333 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00242 (20220) covalent geometry : angle 0.44748 (27404) hydrogen bonds : bond 0.02798 ( 1108) hydrogen bonds : angle 3.82317 ( 3168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.677 Fit side-chains REVERT: A 161 PHE cc_start: 0.7020 (m-80) cc_final: 0.6742 (m-80) REVERT: A 193 ARG cc_start: 0.8180 (mtp180) cc_final: 0.7966 (mtp85) REVERT: A 221 LYS cc_start: 0.7292 (mttm) cc_final: 0.6760 (mmtp) REVERT: A 289 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7506 (mp0) REVERT: A 308 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7414 (tp) REVERT: A 309 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 392 ARG cc_start: 0.6603 (ttt90) cc_final: 0.6196 (ttp-170) REVERT: A 433 MET cc_start: 0.6617 (mmp) cc_final: 0.5704 (ttp) REVERT: A 595 ASP cc_start: 0.5810 (m-30) cc_final: 0.5176 (t0) REVERT: A 613 GLN cc_start: 0.6561 (mm-40) cc_final: 0.5404 (mp10) REVERT: A 679 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6450 (mtm110) REVERT: A 687 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6822 (mtm-85) REVERT: A 701 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7844 (mm-30) REVERT: A 709 GLU cc_start: 0.7421 (tt0) cc_final: 0.6159 (mt-10) REVERT: B 161 PHE cc_start: 0.7029 (m-80) cc_final: 0.6750 (m-80) REVERT: B 193 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7974 (mtp85) REVERT: B 221 LYS cc_start: 0.7247 (mttm) cc_final: 0.6705 (mmtp) REVERT: B 289 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7513 (mp0) REVERT: B 308 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7421 (tp) REVERT: B 309 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 392 ARG cc_start: 0.6596 (ttt90) cc_final: 0.6193 (ttp-170) REVERT: B 433 MET cc_start: 0.6645 (mmp) cc_final: 0.5727 (ttp) REVERT: B 595 ASP cc_start: 0.5780 (m-30) cc_final: 0.5151 (t0) REVERT: B 613 GLN cc_start: 0.6575 (mm-40) cc_final: 0.5407 (mp10) REVERT: B 679 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6457 (mtm110) REVERT: B 687 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6817 (mtm-85) REVERT: B 701 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7840 (mm-30) REVERT: B 709 GLU cc_start: 0.7433 (tt0) cc_final: 0.6162 (mt-10) REVERT: C 161 PHE cc_start: 0.7076 (m-80) cc_final: 0.6788 (m-80) REVERT: C 193 ARG cc_start: 0.8196 (mtp180) cc_final: 0.7984 (mtp85) REVERT: C 221 LYS cc_start: 0.7237 (mttm) cc_final: 0.6704 (mmtp) REVERT: C 289 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7538 (mp0) REVERT: C 308 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7452 (tp) REVERT: C 309 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7433 (mm-30) REVERT: C 392 ARG cc_start: 0.6590 (ttt90) cc_final: 0.6186 (ttp-170) REVERT: C 433 MET cc_start: 0.6602 (mmp) cc_final: 0.5693 (ttp) REVERT: C 595 ASP cc_start: 0.5756 (m-30) cc_final: 0.5130 (t0) REVERT: C 613 GLN cc_start: 0.6565 (mm-40) cc_final: 0.5398 (mp10) REVERT: C 679 ARG cc_start: 0.7115 (mtt180) cc_final: 0.6455 (mtm110) REVERT: C 687 ARG cc_start: 0.7426 (mtt180) cc_final: 0.6820 (mtm-85) REVERT: C 701 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7861 (mm-30) REVERT: C 709 GLU cc_start: 0.7441 (tt0) cc_final: 0.6168 (mt-10) REVERT: D 161 PHE cc_start: 0.7037 (m-80) cc_final: 0.6758 (m-80) REVERT: D 193 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7969 (mtp85) REVERT: D 221 LYS cc_start: 0.7243 (mttm) cc_final: 0.6710 (mmtp) REVERT: D 289 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7522 (mp0) REVERT: D 308 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7443 (tp) REVERT: D 309 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7422 (mm-30) REVERT: D 392 ARG cc_start: 0.6616 (ttt90) cc_final: 0.6208 (ttp-170) REVERT: D 433 MET cc_start: 0.6603 (mmp) cc_final: 0.5692 (ttp) REVERT: D 595 ASP cc_start: 0.5734 (m-30) cc_final: 0.5112 (t0) REVERT: D 613 GLN cc_start: 0.6572 (mm-40) cc_final: 0.5401 (mp10) REVERT: D 679 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6459 (mtm110) REVERT: D 687 ARG cc_start: 0.7447 (mtt180) cc_final: 0.6840 (mtm-85) REVERT: D 701 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7887 (mm-30) REVERT: D 709 GLU cc_start: 0.7436 (tt0) cc_final: 0.6156 (mt-10) outliers start: 41 outliers final: 23 residues processed: 278 average time/residue: 0.5509 time to fit residues: 173.5389 Evaluate side-chains 280 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 1 optimal weight: 0.0060 chunk 148 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 121 optimal weight: 0.0980 chunk 122 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.162573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124141 restraints weight = 22707.838| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.22 r_work: 0.3370 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20220 Z= 0.092 Angle : 0.447 7.604 27404 Z= 0.228 Chirality : 0.037 0.126 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.638 58.560 2852 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.86 % Allowed : 12.60 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 2.02 (0.17), residues: 2392 helix: 2.07 (0.14), residues: 1484 sheet: 0.50 (0.52), residues: 100 loop : 0.15 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 339 TYR 0.010 0.001 TYR A 228 PHE 0.020 0.001 PHE A 405 TRP 0.030 0.001 TRP B 333 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00212 (20220) covalent geometry : angle 0.44679 (27404) hydrogen bonds : bond 0.02669 ( 1108) hydrogen bonds : angle 3.80723 ( 3168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7012 (mp0) REVERT: A 161 PHE cc_start: 0.7040 (m-80) cc_final: 0.6772 (m-80) REVERT: A 193 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7974 (mtp85) REVERT: A 221 LYS cc_start: 0.7255 (mttm) cc_final: 0.6781 (mmtp) REVERT: A 289 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7504 (mp0) REVERT: A 308 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7399 (tp) REVERT: A 309 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7398 (mm-30) REVERT: A 392 ARG cc_start: 0.6626 (ttt90) cc_final: 0.6225 (ttp-170) REVERT: A 433 MET cc_start: 0.6572 (mmp) cc_final: 0.5880 (mmm) REVERT: A 595 ASP cc_start: 0.5840 (m-30) cc_final: 0.5211 (t0) REVERT: A 613 GLN cc_start: 0.6580 (mm-40) cc_final: 0.5236 (mp10) REVERT: A 679 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6430 (mtm110) REVERT: A 687 ARG cc_start: 0.7421 (mtt180) cc_final: 0.6829 (mtm-85) REVERT: A 690 LYS cc_start: 0.8149 (tttp) cc_final: 0.7907 (tttt) REVERT: A 701 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7861 (mm-30) REVERT: A 709 GLU cc_start: 0.7327 (tt0) cc_final: 0.6227 (mt-10) REVERT: B 91 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7008 (mp0) REVERT: B 161 PHE cc_start: 0.7038 (m-80) cc_final: 0.6771 (m-80) REVERT: B 178 GLN cc_start: 0.7427 (mt0) cc_final: 0.7201 (pm20) REVERT: B 193 ARG cc_start: 0.8173 (mtp180) cc_final: 0.7963 (mtp85) REVERT: B 221 LYS cc_start: 0.7265 (mttm) cc_final: 0.6766 (mmtp) REVERT: B 289 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7523 (mp0) REVERT: B 308 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7423 (tp) REVERT: B 309 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7418 (mm-30) REVERT: B 392 ARG cc_start: 0.6634 (ttt90) cc_final: 0.6228 (ttp-170) REVERT: B 433 MET cc_start: 0.6583 (mmp) cc_final: 0.5893 (mmm) REVERT: B 595 ASP cc_start: 0.5791 (m-30) cc_final: 0.5172 (t0) REVERT: B 613 GLN cc_start: 0.6588 (mm-40) cc_final: 0.5238 (mp10) REVERT: B 679 ARG cc_start: 0.7068 (mtt180) cc_final: 0.6439 (mtm110) REVERT: B 687 ARG cc_start: 0.7406 (mtt180) cc_final: 0.6818 (mtm-85) REVERT: B 690 LYS cc_start: 0.8148 (tttp) cc_final: 0.7911 (tttt) REVERT: B 701 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7859 (mm-30) REVERT: B 709 GLU cc_start: 0.7367 (tt0) cc_final: 0.6254 (mt-10) REVERT: C 161 PHE cc_start: 0.7064 (m-80) cc_final: 0.6788 (m-80) REVERT: C 193 ARG cc_start: 0.8211 (mtp180) cc_final: 0.8003 (mtp85) REVERT: C 221 LYS cc_start: 0.7238 (mttm) cc_final: 0.6758 (mmtp) REVERT: C 289 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7548 (mp0) REVERT: C 308 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7430 (tp) REVERT: C 309 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7426 (mm-30) REVERT: C 392 ARG cc_start: 0.6629 (ttt90) cc_final: 0.6223 (ttp-170) REVERT: C 433 MET cc_start: 0.6561 (mmp) cc_final: 0.5872 (mmm) REVERT: C 595 ASP cc_start: 0.5775 (m-30) cc_final: 0.5155 (t0) REVERT: C 613 GLN cc_start: 0.6586 (mm-40) cc_final: 0.5238 (mp10) REVERT: C 679 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6437 (mtm110) REVERT: C 687 ARG cc_start: 0.7412 (mtt180) cc_final: 0.6812 (mtm-85) REVERT: C 690 LYS cc_start: 0.8134 (tttp) cc_final: 0.7900 (tttt) REVERT: C 701 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7867 (mm-30) REVERT: C 709 GLU cc_start: 0.7327 (tt0) cc_final: 0.6230 (mt-10) REVERT: D 161 PHE cc_start: 0.7038 (m-80) cc_final: 0.6772 (m-80) REVERT: D 178 GLN cc_start: 0.7444 (mt0) cc_final: 0.7218 (pm20) REVERT: D 193 ARG cc_start: 0.8191 (mtp180) cc_final: 0.7982 (mtp85) REVERT: D 221 LYS cc_start: 0.7256 (mttm) cc_final: 0.6779 (mmtp) REVERT: D 289 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7521 (mp0) REVERT: D 308 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7439 (tp) REVERT: D 309 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7431 (mm-30) REVERT: D 392 ARG cc_start: 0.6643 (ttt90) cc_final: 0.6234 (ttp-170) REVERT: D 433 MET cc_start: 0.6557 (mmp) cc_final: 0.5867 (mmm) REVERT: D 595 ASP cc_start: 0.5744 (m-30) cc_final: 0.5129 (t0) REVERT: D 613 GLN cc_start: 0.6580 (mm-40) cc_final: 0.5232 (mp10) REVERT: D 679 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6445 (mtm110) REVERT: D 687 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6840 (mtm-85) REVERT: D 690 LYS cc_start: 0.8141 (tttp) cc_final: 0.7897 (tttt) REVERT: D 701 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7870 (mm-30) REVERT: D 709 GLU cc_start: 0.7360 (tt0) cc_final: 0.6247 (mt-10) outliers start: 39 outliers final: 27 residues processed: 282 average time/residue: 0.5680 time to fit residues: 182.4842 Evaluate side-chains 282 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 251 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 621 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.161338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121876 restraints weight = 22671.986| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.29 r_work: 0.3354 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20220 Z= 0.107 Angle : 0.452 7.334 27404 Z= 0.232 Chirality : 0.037 0.127 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.727 59.745 2852 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.72 % Allowed : 12.55 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.99 (0.17), residues: 2392 helix: 2.04 (0.13), residues: 1484 sheet: 0.42 (0.51), residues: 100 loop : 0.14 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 339 TYR 0.013 0.001 TYR A 228 PHE 0.021 0.001 PHE A 405 TRP 0.032 0.001 TRP C 333 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00259 (20220) covalent geometry : angle 0.45244 (27404) hydrogen bonds : bond 0.02797 ( 1108) hydrogen bonds : angle 3.82832 ( 3168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7050 (mp0) REVERT: A 161 PHE cc_start: 0.7042 (m-80) cc_final: 0.6773 (m-80) REVERT: A 178 GLN cc_start: 0.7466 (mt0) cc_final: 0.7232 (pm20) REVERT: A 221 LYS cc_start: 0.7273 (mttm) cc_final: 0.6789 (mmtp) REVERT: A 289 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7503 (mp0) REVERT: A 308 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7530 (tp) REVERT: A 309 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7422 (mm-30) REVERT: A 392 ARG cc_start: 0.6631 (ttt90) cc_final: 0.6221 (ttp-170) REVERT: A 433 MET cc_start: 0.6593 (mmp) cc_final: 0.5871 (mmm) REVERT: A 595 ASP cc_start: 0.5854 (m-30) cc_final: 0.5217 (t0) REVERT: A 613 GLN cc_start: 0.6743 (mm-40) cc_final: 0.5286 (mp10) REVERT: A 679 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6493 (mtm110) REVERT: A 687 ARG cc_start: 0.7384 (mtt180) cc_final: 0.6802 (mtm-85) REVERT: A 690 LYS cc_start: 0.8148 (tttp) cc_final: 0.7918 (tttt) REVERT: A 701 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7872 (mm-30) REVERT: A 709 GLU cc_start: 0.7327 (tt0) cc_final: 0.6196 (mt-10) REVERT: B 91 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7017 (mp0) REVERT: B 161 PHE cc_start: 0.7041 (m-80) cc_final: 0.6774 (m-80) REVERT: B 221 LYS cc_start: 0.7258 (mttm) cc_final: 0.6756 (mmtp) REVERT: B 289 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7517 (mp0) REVERT: B 308 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7534 (tp) REVERT: B 309 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 392 ARG cc_start: 0.6639 (ttt90) cc_final: 0.6231 (ttp-170) REVERT: B 433 MET cc_start: 0.6616 (mmp) cc_final: 0.5894 (mmm) REVERT: B 595 ASP cc_start: 0.5807 (m-30) cc_final: 0.5177 (t0) REVERT: B 613 GLN cc_start: 0.6754 (mm-40) cc_final: 0.5292 (mp10) REVERT: B 679 ARG cc_start: 0.7098 (mtt180) cc_final: 0.6484 (mtm110) REVERT: B 687 ARG cc_start: 0.7389 (mtt180) cc_final: 0.6811 (mtm-85) REVERT: B 690 LYS cc_start: 0.8141 (tttp) cc_final: 0.7919 (tttt) REVERT: B 701 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7876 (mm-30) REVERT: B 709 GLU cc_start: 0.7393 (tt0) cc_final: 0.6176 (mt-10) REVERT: C 161 PHE cc_start: 0.7085 (m-80) cc_final: 0.6813 (m-80) REVERT: C 178 GLN cc_start: 0.7488 (mt0) cc_final: 0.7255 (pm20) REVERT: C 221 LYS cc_start: 0.7241 (mttm) cc_final: 0.6768 (mmtp) REVERT: C 289 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7544 (mp0) REVERT: C 308 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7539 (tp) REVERT: C 309 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7431 (mm-30) REVERT: C 392 ARG cc_start: 0.6618 (ttt90) cc_final: 0.6207 (ttp-170) REVERT: C 433 MET cc_start: 0.6588 (mmp) cc_final: 0.5869 (mmm) REVERT: C 595 ASP cc_start: 0.5793 (m-30) cc_final: 0.5165 (t0) REVERT: C 613 GLN cc_start: 0.6751 (mm-40) cc_final: 0.5291 (mp10) REVERT: C 679 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6492 (mtm110) REVERT: C 687 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6792 (mtm-85) REVERT: C 690 LYS cc_start: 0.8131 (tttp) cc_final: 0.7914 (tttt) REVERT: C 701 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7880 (mm-30) REVERT: C 709 GLU cc_start: 0.7389 (tt0) cc_final: 0.6211 (mt-10) REVERT: D 161 PHE cc_start: 0.7066 (m-80) cc_final: 0.6799 (m-80) REVERT: D 221 LYS cc_start: 0.7267 (mttm) cc_final: 0.6775 (mmtp) REVERT: D 289 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7521 (mp0) REVERT: D 308 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7547 (tp) REVERT: D 309 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7433 (mm-30) REVERT: D 392 ARG cc_start: 0.6655 (ttt90) cc_final: 0.6242 (ttp-170) REVERT: D 433 MET cc_start: 0.6572 (mmp) cc_final: 0.5852 (mmm) REVERT: D 595 ASP cc_start: 0.5773 (m-30) cc_final: 0.5147 (t0) REVERT: D 613 GLN cc_start: 0.6757 (mm-40) cc_final: 0.5295 (mp10) REVERT: D 679 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6496 (mtm110) REVERT: D 687 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6824 (mtm-85) REVERT: D 690 LYS cc_start: 0.8139 (tttp) cc_final: 0.7909 (tttt) REVERT: D 701 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7884 (mm-30) REVERT: D 709 GLU cc_start: 0.7344 (tt0) cc_final: 0.6198 (mt-10) outliers start: 36 outliers final: 23 residues processed: 280 average time/residue: 0.5685 time to fit residues: 180.6021 Evaluate side-chains 277 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 250 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 209 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121212 restraints weight = 22871.997| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.29 r_work: 0.3338 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20220 Z= 0.115 Angle : 0.472 7.146 27404 Z= 0.238 Chirality : 0.037 0.126 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.810 61.692 2852 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.57 % Allowed : 12.64 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.94 (0.17), residues: 2392 helix: 2.01 (0.13), residues: 1484 sheet: 0.32 (0.51), residues: 100 loop : 0.14 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 339 TYR 0.013 0.001 TYR A 228 PHE 0.022 0.001 PHE A 405 TRP 0.035 0.001 TRP B 333 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00278 (20220) covalent geometry : angle 0.47229 (27404) hydrogen bonds : bond 0.02859 ( 1108) hydrogen bonds : angle 3.86870 ( 3168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.804 Fit side-chains REVERT: A 91 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7062 (mp0) REVERT: A 161 PHE cc_start: 0.7131 (m-80) cc_final: 0.6858 (m-80) REVERT: A 221 LYS cc_start: 0.7291 (mttm) cc_final: 0.6812 (mmtp) REVERT: A 289 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 308 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7582 (tp) REVERT: A 309 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7433 (mm-30) REVERT: A 392 ARG cc_start: 0.6621 (ttt90) cc_final: 0.6288 (ttp-170) REVERT: A 433 MET cc_start: 0.6728 (mmp) cc_final: 0.5976 (mmm) REVERT: A 595 ASP cc_start: 0.5896 (m-30) cc_final: 0.5237 (t0) REVERT: A 679 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6598 (mtm110) REVERT: A 687 ARG cc_start: 0.7383 (mtt180) cc_final: 0.6808 (mtm-85) REVERT: A 690 LYS cc_start: 0.8154 (tttp) cc_final: 0.7882 (tttt) REVERT: A 701 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7858 (mm-30) REVERT: A 709 GLU cc_start: 0.7471 (tt0) cc_final: 0.6222 (mt-10) REVERT: B 91 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7061 (mp0) REVERT: B 161 PHE cc_start: 0.7119 (m-80) cc_final: 0.6850 (m-80) REVERT: B 221 LYS cc_start: 0.7246 (mttm) cc_final: 0.6760 (mmtp) REVERT: B 289 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7532 (mp0) REVERT: B 308 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7566 (tp) REVERT: B 309 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 392 ARG cc_start: 0.6614 (ttt90) cc_final: 0.6284 (ttp-170) REVERT: B 433 MET cc_start: 0.6689 (mmp) cc_final: 0.5938 (mmm) REVERT: B 595 ASP cc_start: 0.5876 (m-30) cc_final: 0.5223 (t0) REVERT: B 679 ARG cc_start: 0.7159 (mtt180) cc_final: 0.6597 (mtm110) REVERT: B 687 ARG cc_start: 0.7417 (mtt180) cc_final: 0.6828 (mtm-85) REVERT: B 690 LYS cc_start: 0.8141 (tttp) cc_final: 0.7873 (tttt) REVERT: B 701 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7853 (mm-30) REVERT: B 709 GLU cc_start: 0.7490 (tt0) cc_final: 0.6213 (mt-10) REVERT: C 91 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7066 (mp0) REVERT: C 161 PHE cc_start: 0.7151 (m-80) cc_final: 0.6872 (m-80) REVERT: C 178 GLN cc_start: 0.7480 (mt0) cc_final: 0.7252 (pm20) REVERT: C 221 LYS cc_start: 0.7278 (mttm) cc_final: 0.6797 (mmtp) REVERT: C 289 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7553 (mp0) REVERT: C 308 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7589 (tp) REVERT: C 309 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7449 (mm-30) REVERT: C 392 ARG cc_start: 0.6609 (ttt90) cc_final: 0.6276 (ttp-170) REVERT: C 433 MET cc_start: 0.6674 (mmp) cc_final: 0.5923 (mmm) REVERT: C 595 ASP cc_start: 0.5870 (m-30) cc_final: 0.5215 (t0) REVERT: C 679 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6607 (mtm110) REVERT: C 687 ARG cc_start: 0.7393 (mtt180) cc_final: 0.6806 (mtm-85) REVERT: C 690 LYS cc_start: 0.8132 (tttp) cc_final: 0.7868 (tttt) REVERT: C 701 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7864 (mm-30) REVERT: C 709 GLU cc_start: 0.7470 (tt0) cc_final: 0.6222 (mt-10) REVERT: D 91 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7062 (mp0) REVERT: D 161 PHE cc_start: 0.7160 (m-80) cc_final: 0.6883 (m-80) REVERT: D 221 LYS cc_start: 0.7275 (mttm) cc_final: 0.6787 (mmtp) REVERT: D 289 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7542 (mp0) REVERT: D 308 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7586 (tp) REVERT: D 309 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 392 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6302 (ttp-170) REVERT: D 433 MET cc_start: 0.6650 (mmp) cc_final: 0.5901 (mmm) REVERT: D 595 ASP cc_start: 0.5830 (m-30) cc_final: 0.5181 (t0) REVERT: D 679 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6609 (mtm110) REVERT: D 687 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6836 (mtm-85) REVERT: D 690 LYS cc_start: 0.8147 (tttp) cc_final: 0.7876 (tttt) REVERT: D 701 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7870 (mm-30) REVERT: D 709 GLU cc_start: 0.7483 (tt0) cc_final: 0.6214 (mt-10) outliers start: 33 outliers final: 25 residues processed: 265 average time/residue: 0.5513 time to fit residues: 166.7315 Evaluate side-chains 267 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 621 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 0.0570 chunk 162 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 205 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122823 restraints weight = 22771.767| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.28 r_work: 0.3360 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20220 Z= 0.100 Angle : 0.449 7.041 27404 Z= 0.230 Chirality : 0.037 0.126 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.685 59.088 2852 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.62 % Allowed : 12.45 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 2.01 (0.17), residues: 2392 helix: 2.07 (0.14), residues: 1484 sheet: 0.29 (0.51), residues: 100 loop : 0.16 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 175 TYR 0.011 0.001 TYR A 228 PHE 0.021 0.001 PHE A 405 TRP 0.037 0.001 TRP D 333 HIS 0.003 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00236 (20220) covalent geometry : angle 0.44928 (27404) hydrogen bonds : bond 0.02736 ( 1108) hydrogen bonds : angle 3.81316 ( 3168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7023.37 seconds wall clock time: 120 minutes 10.68 seconds (7210.68 seconds total)