Starting phenix.real_space_refine on Tue May 20 07:47:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3y_44160/05_2025/9b3y_44160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3y_44160/05_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_44160/05_2025/9b3y_44160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3y_44160/05_2025/9b3y_44160.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3y_44160/05_2025/9b3y_44160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3y_44160/05_2025/9b3y_44160.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} 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: C, B, D Time building chain proxies: 10.76, per 1000 atoms: 0.54 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: 4.37 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.84 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: 6.15 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.010 Normalize map: mean=0, sd=1: 1.800 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: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 40.550 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.230 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (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 TRP 0.108 0.019 TRP A 509 HIS 0.010 0.003 HIS D 363 PHE 0.058 0.011 PHE D 467 TYR 0.111 0.021 TYR A 447 ARG 0.011 0.001 ARG B 317 Details of bonding type rmsd hydrogen bonds : bond 0.15941 ( 1108) hydrogen bonds : angle 6.72771 ( 3168) covalent geometry : bond 0.01225 (20220) covalent geometry : angle 1.79154 (27404) *********************** 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 : 2.054 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: 0.6426 (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 433 MET cc_start: 0.6896 (mmm) cc_final: 0.6692 (mmp) REVERT: A 470 SER cc_start: 0.7918 (m) cc_final: 0.7650 (p) REVERT: A 530 GLN cc_start: 0.6403 (pt0) cc_final: 0.5039 (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: 0.7763 (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: 0.7305 (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: 0.7478 (mtp-110) 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: 0.7648 (p) REVERT: B 530 GLN cc_start: 0.6402 (pt0) cc_final: 0.5038 (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: 0.6336 (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 433 MET cc_start: 0.6896 (mmm) cc_final: 0.6693 (mmp) REVERT: C 470 SER cc_start: 0.7917 (m) cc_final: 0.7649 (p) REVERT: C 530 GLN cc_start: 0.6401 (pt0) cc_final: 0.5038 (tp-100) REVERT: C 595 ASP cc_start: 0.5666 (m-30) cc_final: 0.5225 (t0) REVERT: C 645 MET cc_start: 0.8023 (mtt) cc_final: 0.7765 (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: 0.7004 (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 433 MET cc_start: 0.6897 (mmm) cc_final: 0.6693 (mmp) REVERT: D 470 SER cc_start: 0.7918 (m) cc_final: 0.7650 (p) REVERT: D 530 GLN cc_start: 0.6402 (pt0) cc_final: 0.5038 (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: 0.7764 (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: 0.6336 (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: 1.3134 time to fit residues: 576.5675 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 : 2.154 ------------------------------------------------------------------------------- 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 202 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 294 GLN B 141 GLN B 294 GLN C 141 GLN D 141 GLN D 294 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122864 restraints weight = 22504.983| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.20 r_work: 0.3347 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2039 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= 0.131 Angle : 0.548 5.828 27404 Z= 0.296 Chirality : 0.040 0.173 3100 Planarity : 0.004 0.042 3348 Dihedral : 9.669 74.953 2868 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.43 % Allowed : 6.97 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2392 helix: 1.02 (0.13), residues: 1488 sheet: -0.04 (0.48), residues: 116 loop : 0.38 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 333 HIS 0.006 0.001 HIS D 313 PHE 0.017 0.001 PHE A 467 TYR 0.016 0.001 TYR A 403 ARG 0.004 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1108) hydrogen bonds : angle 4.33444 ( 3168) covalent geometry : bond 0.00308 (20220) covalent geometry : angle 0.54817 (27404) *********************** 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 343 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 313 time to evaluate : 1.975 Fit side-chains REVERT: A 108 ASP cc_start: 0.6357 (m-30) cc_final: 0.5961 (p0) REVERT: A 151 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6564 (tt) REVERT: A 161 PHE cc_start: 0.6910 (m-80) cc_final: 0.6207 (m-80) REVERT: A 197 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7382 (tpt-90) REVERT: A 221 LYS cc_start: 0.7314 (mttm) cc_final: 0.6843 (mmtp) REVERT: A 240 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7668 (mt-10) REVERT: A 277 MET cc_start: 0.6530 (mtp) cc_final: 0.6284 (mtp) REVERT: A 289 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7519 (mp0) REVERT: A 392 ARG cc_start: 0.6580 (ttt90) cc_final: 0.6197 (ttp-170) REVERT: A 530 GLN cc_start: 0.6252 (pt0) cc_final: 0.4793 (tp-100) REVERT: A 595 ASP cc_start: 0.5521 (m-30) cc_final: 0.4980 (t0) REVERT: A 645 MET cc_start: 0.7438 (mtt) cc_final: 0.7209 (mtp) REVERT: A 679 ARG cc_start: 0.7106 (mtt180) cc_final: 0.6293 (mtm110) REVERT: A 687 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6683 (mtm-85) REVERT: A 701 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7868 (mm-30) REVERT: B 108 ASP cc_start: 0.6355 (m-30) cc_final: 0.5954 (p0) REVERT: B 151 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6570 (tt) REVERT: B 161 PHE cc_start: 0.6903 (m-80) cc_final: 0.6196 (m-80) REVERT: B 197 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7367 (tpt-90) REVERT: B 221 LYS cc_start: 0.7335 (mttm) cc_final: 0.6867 (mmtp) REVERT: B 240 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 277 MET cc_start: 0.6520 (mtp) cc_final: 0.6277 (mtp) REVERT: B 289 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7525 (mp0) REVERT: B 392 ARG cc_start: 0.6575 (ttt90) cc_final: 0.6192 (ttp-170) REVERT: B 530 GLN cc_start: 0.6264 (pt0) cc_final: 0.4809 (tp-100) REVERT: B 595 ASP cc_start: 0.5495 (m-30) cc_final: 0.4954 (t0) REVERT: B 645 MET cc_start: 0.7423 (mtt) cc_final: 0.7195 (mtp) REVERT: B 679 ARG cc_start: 0.7146 (mtt180) cc_final: 0.6319 (mtm110) REVERT: B 687 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6639 (mtm-85) REVERT: B 701 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7870 (mm-30) REVERT: C 108 ASP cc_start: 0.6361 (m-30) cc_final: 0.5961 (p0) REVERT: C 151 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6573 (tt) REVERT: C 161 PHE cc_start: 0.6899 (m-80) cc_final: 0.6195 (m-80) REVERT: C 197 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7403 (tpt-90) REVERT: C 221 LYS cc_start: 0.7313 (mttm) cc_final: 0.6842 (mmtp) REVERT: C 240 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 277 MET cc_start: 0.6547 (mtp) cc_final: 0.6300 (mtp) REVERT: C 289 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7534 (mp0) REVERT: C 392 ARG cc_start: 0.6583 (ttt90) cc_final: 0.6197 (ttp-170) REVERT: C 530 GLN cc_start: 0.6261 (pt0) cc_final: 0.4806 (tp-100) REVERT: C 595 ASP cc_start: 0.5507 (m-30) cc_final: 0.4966 (t0) REVERT: C 645 MET cc_start: 0.7452 (mtt) cc_final: 0.7219 (mtp) REVERT: C 679 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6317 (mtm110) REVERT: C 687 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6679 (mtm-85) REVERT: C 701 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7875 (mm-30) REVERT: D 108 ASP cc_start: 0.6353 (m-30) cc_final: 0.5954 (p0) REVERT: D 151 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6553 (tt) REVERT: D 161 PHE cc_start: 0.6911 (m-80) cc_final: 0.6198 (m-80) REVERT: D 197 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7399 (tpt-90) REVERT: D 221 LYS cc_start: 0.7322 (mttm) cc_final: 0.6850 (mmtp) REVERT: D 240 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 277 MET cc_start: 0.6546 (mtp) cc_final: 0.6298 (mtp) REVERT: D 289 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7522 (mp0) REVERT: D 392 ARG cc_start: 0.6601 (ttt90) cc_final: 0.6219 (ttp-170) REVERT: D 530 GLN cc_start: 0.6262 (pt0) cc_final: 0.4799 (tp-100) REVERT: D 595 ASP cc_start: 0.5543 (m-30) cc_final: 0.4994 (t0) REVERT: D 645 MET cc_start: 0.7474 (mtt) cc_final: 0.7240 (mtp) REVERT: D 679 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6312 (mtm110) REVERT: D 687 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6675 (mtm-85) REVERT: D 701 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7862 (mm-30) outliers start: 30 outliers final: 0 residues processed: 331 average time/residue: 1.2037 time to fit residues: 452.1899 Evaluate side-chains 236 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 2.105 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.0170 chunk 206 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 230 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123253 restraints weight = 22522.245| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.25 r_work: 0.3342 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20220 Z= 0.111 Angle : 0.476 6.923 27404 Z= 0.254 Chirality : 0.038 0.152 3100 Planarity : 0.004 0.041 3348 Dihedral : 8.982 59.969 2868 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.62 % Allowed : 10.21 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.17), residues: 2392 helix: 1.51 (0.13), residues: 1496 sheet: 0.00 (0.49), residues: 116 loop : 0.34 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 333 HIS 0.004 0.001 HIS C 251 PHE 0.015 0.001 PHE C 467 TYR 0.009 0.001 TYR A 525 ARG 0.007 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 1108) hydrogen bonds : angle 4.10338 ( 3168) covalent geometry : bond 0.00266 (20220) covalent geometry : angle 0.47578 (27404) *********************** 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 294 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 2.019 Fit side-chains REVERT: A 151 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6732 (tt) REVERT: A 161 PHE cc_start: 0.6967 (m-80) cc_final: 0.6487 (m-80) REVERT: A 221 LYS cc_start: 0.7291 (mttm) cc_final: 0.6911 (mmtp) REVERT: A 240 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7622 (mt-10) REVERT: A 277 MET cc_start: 0.6537 (mtp) cc_final: 0.6241 (mtp) REVERT: A 289 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7519 (mp0) REVERT: A 309 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 392 ARG cc_start: 0.6561 (ttt90) cc_final: 0.6135 (ttp-170) REVERT: A 530 GLN cc_start: 0.6091 (pt0) cc_final: 0.4706 (mm-40) REVERT: A 595 ASP cc_start: 0.5640 (m-30) cc_final: 0.5047 (t0) REVERT: A 679 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6297 (mtm110) REVERT: A 687 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6637 (mtm-85) REVERT: A 701 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7842 (mm-30) REVERT: A 709 GLU cc_start: 0.7503 (tt0) cc_final: 0.6136 (mt-10) REVERT: B 151 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6727 (tt) REVERT: B 161 PHE cc_start: 0.6946 (m-80) cc_final: 0.6501 (m-80) REVERT: B 221 LYS cc_start: 0.7298 (mttm) cc_final: 0.6913 (mmtp) REVERT: B 240 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 277 MET cc_start: 0.6518 (mtp) cc_final: 0.6226 (mtp) REVERT: B 289 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7534 (mp0) REVERT: B 309 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7468 (mm-30) REVERT: B 392 ARG cc_start: 0.6547 (ttt90) cc_final: 0.6119 (ttp-170) REVERT: B 530 GLN cc_start: 0.6097 (pt0) cc_final: 0.4710 (mm-40) REVERT: B 595 ASP cc_start: 0.5653 (m-30) cc_final: 0.5057 (t0) REVERT: B 679 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6328 (mtm110) REVERT: B 687 ARG cc_start: 0.7388 (mtt180) cc_final: 0.6603 (mtm-85) REVERT: B 701 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7839 (mm-30) REVERT: B 709 GLU cc_start: 0.7505 (tt0) cc_final: 0.6141 (mt-10) REVERT: C 151 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6720 (tt) REVERT: C 161 PHE cc_start: 0.6978 (m-80) cc_final: 0.6536 (m-80) REVERT: C 221 LYS cc_start: 0.7313 (mttm) cc_final: 0.6935 (mmtp) REVERT: C 240 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7620 (mt-10) REVERT: C 277 MET cc_start: 0.6574 (mtp) cc_final: 0.6281 (mtp) REVERT: C 289 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7545 (mp0) REVERT: C 309 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7492 (mm-30) REVERT: C 392 ARG cc_start: 0.6534 (ttt90) cc_final: 0.6104 (ttp-170) REVERT: C 530 GLN cc_start: 0.6084 (pt0) cc_final: 0.4695 (mm-40) REVERT: C 595 ASP cc_start: 0.5630 (m-30) cc_final: 0.5041 (t0) REVERT: C 679 ARG cc_start: 0.7121 (mtt180) cc_final: 0.6319 (mtm110) REVERT: C 687 ARG cc_start: 0.7410 (mtt180) cc_final: 0.6620 (mtm-85) REVERT: C 701 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7845 (mm-30) REVERT: C 709 GLU cc_start: 0.7494 (tt0) cc_final: 0.6127 (mt-10) REVERT: D 151 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6710 (tt) REVERT: D 161 PHE cc_start: 0.6949 (m-80) cc_final: 0.6513 (m-80) REVERT: D 221 LYS cc_start: 0.7307 (mttm) cc_final: 0.6929 (mmtp) REVERT: D 240 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7633 (mt-10) REVERT: D 277 MET cc_start: 0.6549 (mtp) cc_final: 0.6256 (mtp) REVERT: D 289 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7530 (mp0) REVERT: D 309 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7479 (mm-30) REVERT: D 392 ARG cc_start: 0.6574 (ttt90) cc_final: 0.6147 (ttp-170) REVERT: D 530 GLN cc_start: 0.6077 (pt0) cc_final: 0.4687 (mm-40) REVERT: D 595 ASP cc_start: 0.5640 (m-30) cc_final: 0.5048 (t0) REVERT: D 679 ARG cc_start: 0.7113 (mtt180) cc_final: 0.6324 (mtm110) REVERT: D 687 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6616 (mtm-85) REVERT: D 701 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7840 (mm-30) REVERT: D 709 GLU cc_start: 0.7511 (tt0) cc_final: 0.6145 (mt-10) outliers start: 34 outliers final: 4 residues processed: 278 average time/residue: 1.2090 time to fit residues: 382.6064 Evaluate side-chains 244 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 3.9990 chunk 66 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.157327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.118567 restraints weight = 22949.622| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.26 r_work: 0.3284 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20220 Z= 0.192 Angle : 0.552 6.326 27404 Z= 0.284 Chirality : 0.041 0.146 3100 Planarity : 0.004 0.043 3348 Dihedral : 9.037 79.437 2852 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.48 % Allowed : 10.93 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.17), residues: 2392 helix: 1.36 (0.13), residues: 1500 sheet: -0.56 (0.50), residues: 120 loop : 0.09 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 333 HIS 0.006 0.002 HIS A 521 PHE 0.016 0.002 PHE C 467 TYR 0.010 0.002 TYR A 412 ARG 0.004 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 1108) hydrogen bonds : angle 4.22532 ( 3168) covalent geometry : bond 0.00482 (20220) covalent geometry : angle 0.55201 (27404) *********************** 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 331 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 279 time to evaluate : 2.204 Fit side-chains REVERT: A 161 PHE cc_start: 0.7025 (m-80) cc_final: 0.6571 (m-80) REVERT: A 221 LYS cc_start: 0.7297 (mttm) cc_final: 0.6897 (mmtp) REVERT: A 228 TYR cc_start: 0.7371 (t80) cc_final: 0.6985 (t80) REVERT: A 240 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 289 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7495 (mp0) REVERT: A 308 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7636 (tp) REVERT: A 309 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 392 ARG cc_start: 0.6578 (ttt90) cc_final: 0.6201 (ttp-170) REVERT: A 470 SER cc_start: 0.7775 (m) cc_final: 0.7243 (p) REVERT: A 530 GLN cc_start: 0.6001 (pt0) cc_final: 0.4733 (tp-100) REVERT: A 595 ASP cc_start: 0.5803 (m-30) cc_final: 0.5119 (t0) REVERT: A 609 GLU cc_start: 0.6736 (mt-10) cc_final: 0.5839 (tp30) REVERT: A 647 GLU cc_start: 0.7020 (tt0) cc_final: 0.6793 (pt0) REVERT: A 679 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6362 (mtm110) REVERT: A 687 ARG cc_start: 0.7394 (mtt180) cc_final: 0.6689 (mtm-85) REVERT: A 709 GLU cc_start: 0.7601 (tt0) cc_final: 0.6238 (mt-10) REVERT: B 161 PHE cc_start: 0.7005 (m-80) cc_final: 0.6550 (m-80) REVERT: B 221 LYS cc_start: 0.7314 (mttm) cc_final: 0.6912 (mmtp) REVERT: B 228 TYR cc_start: 0.7375 (t80) cc_final: 0.6986 (t80) REVERT: B 289 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7517 (mp0) REVERT: B 308 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7628 (tp) REVERT: B 309 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 392 ARG cc_start: 0.6585 (ttt90) cc_final: 0.6210 (ttp-170) REVERT: B 470 SER cc_start: 0.7787 (m) cc_final: 0.7252 (p) REVERT: B 530 GLN cc_start: 0.6030 (pt0) cc_final: 0.4756 (tp-100) REVERT: B 595 ASP cc_start: 0.5777 (m-30) cc_final: 0.5099 (t0) REVERT: B 609 GLU cc_start: 0.6725 (mt-10) cc_final: 0.5825 (tp30) REVERT: B 647 GLU cc_start: 0.7021 (tt0) cc_final: 0.6791 (pt0) REVERT: B 679 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6370 (mtm110) REVERT: B 687 ARG cc_start: 0.7381 (mtt180) cc_final: 0.6687 (mtm-85) REVERT: B 709 GLU cc_start: 0.7616 (tt0) cc_final: 0.6253 (mt-10) REVERT: C 161 PHE cc_start: 0.7027 (m-80) cc_final: 0.6575 (m-80) REVERT: C 221 LYS cc_start: 0.7298 (mttm) cc_final: 0.6901 (mmtp) REVERT: C 228 TYR cc_start: 0.7358 (t80) cc_final: 0.6978 (t80) REVERT: C 240 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 289 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7479 (mp0) REVERT: C 308 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7638 (tp) REVERT: C 309 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7576 (mm-30) REVERT: C 392 ARG cc_start: 0.6570 (ttt90) cc_final: 0.6190 (ttp-170) REVERT: C 470 SER cc_start: 0.7793 (m) cc_final: 0.7262 (p) REVERT: C 530 GLN cc_start: 0.6030 (pt0) cc_final: 0.4752 (tp-100) REVERT: C 595 ASP cc_start: 0.5744 (m-30) cc_final: 0.5073 (t0) REVERT: C 609 GLU cc_start: 0.6735 (mt-10) cc_final: 0.5832 (tp30) REVERT: C 647 GLU cc_start: 0.7023 (tt0) cc_final: 0.6798 (pt0) REVERT: C 679 ARG cc_start: 0.7174 (mtt180) cc_final: 0.6369 (mtm110) REVERT: C 687 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6697 (mtm-85) REVERT: C 709 GLU cc_start: 0.7587 (tt0) cc_final: 0.6217 (mt-10) REVERT: D 161 PHE cc_start: 0.7008 (m-80) cc_final: 0.6557 (m-80) REVERT: D 221 LYS cc_start: 0.7317 (mttm) cc_final: 0.6916 (mmtp) REVERT: D 228 TYR cc_start: 0.7406 (t80) cc_final: 0.7022 (t80) REVERT: D 240 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7711 (mt-10) REVERT: D 289 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7553 (mp0) REVERT: D 308 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7644 (tp) REVERT: D 309 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7579 (mm-30) REVERT: D 392 ARG cc_start: 0.6588 (ttt90) cc_final: 0.6207 (ttp-170) REVERT: D 470 SER cc_start: 0.7783 (m) cc_final: 0.7255 (p) REVERT: D 530 GLN cc_start: 0.6025 (pt0) cc_final: 0.4752 (tp-100) REVERT: D 595 ASP cc_start: 0.5765 (m-30) cc_final: 0.5090 (t0) REVERT: D 609 GLU cc_start: 0.6721 (mt-10) cc_final: 0.5822 (tp30) REVERT: D 647 GLU cc_start: 0.7027 (tt0) cc_final: 0.6793 (pt0) REVERT: D 679 ARG cc_start: 0.7177 (mtt180) cc_final: 0.6378 (mtm110) REVERT: D 687 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6717 (mtm-85) REVERT: D 709 GLU cc_start: 0.7590 (tt0) cc_final: 0.6224 (mt-10) outliers start: 52 outliers final: 20 residues processed: 307 average time/residue: 1.2268 time to fit residues: 427.3269 Evaluate side-chains 259 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 178 GLN Chi-restraints excluded: chain A residue 308 ILE 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 158 THR Chi-restraints excluded: chain B residue 178 GLN Chi-restraints excluded: chain B residue 308 ILE 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 158 THR Chi-restraints excluded: chain C residue 178 GLN Chi-restraints excluded: chain C residue 308 ILE 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 158 THR Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 534 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 54 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.158643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118916 restraints weight = 22948.726| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.33 r_work: 0.3297 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20220 Z= 0.144 Angle : 0.495 6.605 27404 Z= 0.256 Chirality : 0.039 0.133 3100 Planarity : 0.004 0.041 3348 Dihedral : 8.513 72.686 2852 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.10 % Allowed : 11.64 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2392 helix: 1.53 (0.13), residues: 1508 sheet: 0.12 (0.54), residues: 100 loop : -0.06 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 333 HIS 0.004 0.001 HIS D 313 PHE 0.013 0.001 PHE D 405 TYR 0.008 0.001 TYR A 525 ARG 0.003 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 1108) hydrogen bonds : angle 4.05438 ( 3168) covalent geometry : bond 0.00357 (20220) covalent geometry : angle 0.49488 (27404) *********************** 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 284 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 2.095 Fit side-chains REVERT: A 161 PHE cc_start: 0.7085 (m-80) cc_final: 0.6694 (m-80) REVERT: A 221 LYS cc_start: 0.7332 (mttm) cc_final: 0.6942 (mmtp) REVERT: A 289 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7484 (mp0) REVERT: A 308 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7631 (tp) REVERT: A 309 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7478 (mm-30) REVERT: A 392 ARG cc_start: 0.6557 (ttt90) cc_final: 0.6181 (ttp-170) REVERT: A 595 ASP cc_start: 0.5859 (m-30) cc_final: 0.5172 (t0) REVERT: A 609 GLU cc_start: 0.6727 (mt-10) cc_final: 0.5740 (tp30) REVERT: A 647 GLU cc_start: 0.7085 (tt0) cc_final: 0.6778 (pt0) REVERT: A 679 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6324 (mtm110) REVERT: A 687 ARG cc_start: 0.7364 (mtt180) cc_final: 0.6699 (mtm-85) REVERT: A 709 GLU cc_start: 0.7581 (tt0) cc_final: 0.6236 (mt-10) REVERT: B 161 PHE cc_start: 0.7041 (m-80) cc_final: 0.6652 (m-80) REVERT: B 221 LYS cc_start: 0.7334 (mttm) cc_final: 0.6937 (mmtp) REVERT: B 289 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7461 (mp0) REVERT: B 308 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7620 (tp) REVERT: B 309 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7466 (mm-30) REVERT: B 392 ARG cc_start: 0.6580 (ttt90) cc_final: 0.6203 (ttp-170) REVERT: B 595 ASP cc_start: 0.5798 (m-30) cc_final: 0.5120 (t0) REVERT: B 609 GLU cc_start: 0.6724 (mt-10) cc_final: 0.5733 (tp30) REVERT: B 647 GLU cc_start: 0.7075 (tt0) cc_final: 0.6718 (pt0) REVERT: B 679 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6307 (mtm110) REVERT: B 687 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6696 (mtm-85) REVERT: B 709 GLU cc_start: 0.7592 (tt0) cc_final: 0.6251 (mt-10) REVERT: C 161 PHE cc_start: 0.7075 (m-80) cc_final: 0.6678 (m-80) REVERT: C 221 LYS cc_start: 0.7318 (mttm) cc_final: 0.6931 (mmtp) REVERT: C 289 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7515 (mp0) REVERT: C 308 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7637 (tp) REVERT: C 309 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 392 ARG cc_start: 0.6570 (ttt90) cc_final: 0.6185 (ttp-170) REVERT: C 595 ASP cc_start: 0.5787 (m-30) cc_final: 0.5113 (t0) REVERT: C 609 GLU cc_start: 0.6735 (mt-10) cc_final: 0.5744 (tp30) REVERT: C 647 GLU cc_start: 0.7073 (tt0) cc_final: 0.6736 (pt0) REVERT: C 679 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6305 (mtm110) REVERT: C 687 ARG cc_start: 0.7379 (mtt180) cc_final: 0.6699 (mtm-85) REVERT: C 709 GLU cc_start: 0.7564 (tt0) cc_final: 0.6216 (mt-10) REVERT: D 161 PHE cc_start: 0.7060 (m-80) cc_final: 0.6672 (m-80) REVERT: D 221 LYS cc_start: 0.7353 (mttm) cc_final: 0.6964 (mmtp) REVERT: D 289 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7475 (mp0) REVERT: D 308 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7630 (tp) REVERT: D 309 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7482 (mm-30) REVERT: D 392 ARG cc_start: 0.6574 (ttt90) cc_final: 0.6192 (ttp-170) REVERT: D 595 ASP cc_start: 0.5817 (m-30) cc_final: 0.5138 (t0) REVERT: D 609 GLU cc_start: 0.6722 (mt-10) cc_final: 0.5736 (tp30) REVERT: D 647 GLU cc_start: 0.7054 (tt0) cc_final: 0.6717 (pt0) REVERT: D 679 ARG cc_start: 0.7129 (mtt180) cc_final: 0.6307 (mtm110) REVERT: D 687 ARG cc_start: 0.7381 (mtt180) cc_final: 0.6705 (mtm-85) REVERT: D 709 GLU cc_start: 0.7573 (tt0) cc_final: 0.6224 (mt-10) outliers start: 44 outliers final: 16 residues processed: 268 average time/residue: 1.1535 time to fit residues: 353.0458 Evaluate side-chains 243 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 463 ILE Chi-restraints excluded: chain A residue 534 LEU 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 463 ILE Chi-restraints excluded: chain B residue 534 LEU 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 461 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 534 LEU 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 534 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 chunk 199 optimal weight: 5.9990 chunk 184 optimal weight: 0.0270 chunk 42 optimal weight: 0.4980 overall best weight: 0.5040 ------------------------------------------------------------------------------- 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 = 0.161597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123065 restraints weight = 22755.371| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.22 r_work: 0.3350 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3006 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= 0.096 Angle : 0.439 5.056 27404 Z= 0.230 Chirality : 0.037 0.181 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.864 58.110 2852 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.91 % Allowed : 11.59 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2392 helix: 1.79 (0.13), residues: 1512 sheet: 0.20 (0.54), residues: 100 loop : 0.09 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 333 HIS 0.003 0.001 HIS C 165 PHE 0.014 0.001 PHE B 405 TYR 0.007 0.001 TYR C 525 ARG 0.005 0.000 ARG C 459 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 1108) hydrogen bonds : angle 3.87940 ( 3168) covalent geometry : bond 0.00218 (20220) covalent geometry : angle 0.43862 (27404) *********************** 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 304 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 2.185 Fit side-chains REVERT: A 161 PHE cc_start: 0.7054 (m-80) cc_final: 0.6726 (m-80) REVERT: A 193 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7975 (mtp85) REVERT: A 221 LYS cc_start: 0.7286 (mttm) cc_final: 0.6751 (mmtp) REVERT: A 289 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7470 (mp0) REVERT: A 308 ILE cc_start: 0.7799 (mm) cc_final: 0.7552 (tp) REVERT: A 309 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7305 (mm-30) REVERT: A 383 GLN cc_start: 0.7485 (tp40) cc_final: 0.7281 (tp-100) REVERT: A 392 ARG cc_start: 0.6539 (ttt90) cc_final: 0.6184 (ttp-170) REVERT: A 595 ASP cc_start: 0.5836 (m-30) cc_final: 0.5184 (t0) REVERT: A 647 GLU cc_start: 0.7250 (tt0) cc_final: 0.6968 (pt0) REVERT: A 679 ARG cc_start: 0.6993 (mtt180) cc_final: 0.6308 (mtm110) REVERT: A 687 ARG cc_start: 0.7363 (mtt180) cc_final: 0.6770 (mtm-85) REVERT: A 709 GLU cc_start: 0.7419 (tt0) cc_final: 0.6153 (mt-10) REVERT: B 161 PHE cc_start: 0.7039 (m-80) cc_final: 0.6707 (m-80) REVERT: B 193 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7965 (mtp85) REVERT: B 221 LYS cc_start: 0.7263 (mttm) cc_final: 0.6724 (mmtp) REVERT: B 289 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7473 (mp0) REVERT: B 308 ILE cc_start: 0.7791 (mm) cc_final: 0.7547 (tp) REVERT: B 309 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 383 GLN cc_start: 0.7520 (tp40) cc_final: 0.7315 (tp-100) REVERT: B 392 ARG cc_start: 0.6538 (ttt90) cc_final: 0.6186 (ttp-170) REVERT: B 595 ASP cc_start: 0.5795 (m-30) cc_final: 0.5150 (t0) REVERT: B 647 GLU cc_start: 0.7256 (tt0) cc_final: 0.6971 (pt0) REVERT: B 679 ARG cc_start: 0.6978 (mtt180) cc_final: 0.6301 (mtm110) REVERT: B 687 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6757 (mtm-85) REVERT: B 709 GLU cc_start: 0.7439 (tt0) cc_final: 0.6173 (mt-10) REVERT: C 161 PHE cc_start: 0.7060 (m-80) cc_final: 0.6730 (m-80) REVERT: C 221 LYS cc_start: 0.7269 (mttm) cc_final: 0.6734 (mmtp) REVERT: C 289 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7496 (mp0) REVERT: C 308 ILE cc_start: 0.7776 (mm) cc_final: 0.7527 (tp) REVERT: C 309 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7324 (mm-30) REVERT: C 383 GLN cc_start: 0.7500 (tp40) cc_final: 0.7298 (tp-100) REVERT: C 392 ARG cc_start: 0.6537 (ttt90) cc_final: 0.6180 (ttp-170) REVERT: C 595 ASP cc_start: 0.5795 (m-30) cc_final: 0.5150 (t0) REVERT: C 647 GLU cc_start: 0.7251 (tt0) cc_final: 0.6965 (pt0) REVERT: C 679 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6296 (mtm110) REVERT: C 687 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6756 (mtm-85) REVERT: C 709 GLU cc_start: 0.7408 (tt0) cc_final: 0.6139 (mt-10) REVERT: D 161 PHE cc_start: 0.7049 (m-80) cc_final: 0.6721 (m-80) REVERT: D 221 LYS cc_start: 0.7285 (mttm) cc_final: 0.6748 (mmtp) REVERT: D 289 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7493 (mp0) REVERT: D 308 ILE cc_start: 0.7801 (mm) cc_final: 0.7551 (tp) REVERT: D 309 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7318 (mm-30) REVERT: D 383 GLN cc_start: 0.7492 (tp40) cc_final: 0.7289 (tp-100) REVERT: D 392 ARG cc_start: 0.6557 (ttt90) cc_final: 0.6198 (ttp-170) REVERT: D 595 ASP cc_start: 0.5770 (m-30) cc_final: 0.5127 (t0) REVERT: D 647 GLU cc_start: 0.7236 (tt0) cc_final: 0.6950 (pt0) REVERT: D 679 ARG cc_start: 0.7003 (mtt180) cc_final: 0.6316 (mtm110) REVERT: D 687 ARG cc_start: 0.7370 (mtt180) cc_final: 0.6760 (mtm-85) REVERT: D 709 GLU cc_start: 0.7434 (tt0) cc_final: 0.6162 (mt-10) outliers start: 40 outliers final: 23 residues processed: 282 average time/residue: 1.1725 time to fit residues: 379.2431 Evaluate side-chains 269 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 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 158 THR Chi-restraints excluded: chain B residue 461 LEU 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 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 158 THR Chi-restraints excluded: chain D residue 461 LEU 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 174 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 chunk 181 optimal weight: 0.5980 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 = 0.160478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120687 restraints weight = 22636.290| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.33 r_work: 0.3323 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3034 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= 0.118 Angle : 0.469 8.171 27404 Z= 0.241 Chirality : 0.038 0.160 3100 Planarity : 0.003 0.041 3348 Dihedral : 7.908 61.023 2852 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.10 % Allowed : 11.02 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2392 helix: 1.85 (0.13), residues: 1484 sheet: 0.12 (0.53), residues: 100 loop : 0.02 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 333 HIS 0.004 0.001 HIS D 251 PHE 0.017 0.001 PHE A 405 TYR 0.007 0.001 TYR B 228 ARG 0.003 0.000 ARG A 460 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 1108) hydrogen bonds : angle 3.87738 ( 3168) covalent geometry : bond 0.00289 (20220) covalent geometry : angle 0.46945 (27404) *********************** 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: 44 poor density : 257 time to evaluate : 2.401 Fit side-chains REVERT: A 122 MET cc_start: 0.6666 (mtt) cc_final: 0.6454 (mtp) REVERT: A 133 ASN cc_start: 0.8030 (t0) cc_final: 0.7816 (t0) REVERT: A 161 PHE cc_start: 0.7063 (m-80) cc_final: 0.6752 (m-80) REVERT: A 221 LYS cc_start: 0.7295 (mttm) cc_final: 0.6761 (mmtp) REVERT: A 289 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7539 (mp0) REVERT: A 308 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7564 (tp) REVERT: A 309 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 392 ARG cc_start: 0.6574 (ttt90) cc_final: 0.6223 (ttp-170) REVERT: A 595 ASP cc_start: 0.5846 (m-30) cc_final: 0.5188 (t0) REVERT: A 647 GLU cc_start: 0.7079 (tt0) cc_final: 0.6744 (pt0) REVERT: A 679 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6390 (mtm110) REVERT: A 687 ARG cc_start: 0.7326 (mtt180) cc_final: 0.6724 (mtm-85) REVERT: A 709 GLU cc_start: 0.7468 (tt0) cc_final: 0.6147 (mt-10) REVERT: B 133 ASN cc_start: 0.8027 (t0) cc_final: 0.7815 (t0) REVERT: B 161 PHE cc_start: 0.7054 (m-80) cc_final: 0.6740 (m-80) REVERT: B 221 LYS cc_start: 0.7275 (mttm) cc_final: 0.6883 (mmtp) REVERT: B 289 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7529 (mp0) REVERT: B 308 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7566 (tp) REVERT: B 309 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7337 (mm-30) REVERT: B 392 ARG cc_start: 0.6579 (ttt90) cc_final: 0.6230 (ttp-170) REVERT: B 595 ASP cc_start: 0.5800 (m-30) cc_final: 0.5149 (t0) REVERT: B 647 GLU cc_start: 0.7077 (tt0) cc_final: 0.6730 (pt0) REVERT: B 679 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6403 (mtm110) REVERT: B 687 ARG cc_start: 0.7319 (mtt180) cc_final: 0.6715 (mtm-85) REVERT: B 709 GLU cc_start: 0.7466 (tt0) cc_final: 0.6150 (mt-10) REVERT: C 133 ASN cc_start: 0.8012 (t0) cc_final: 0.7799 (t0) REVERT: C 161 PHE cc_start: 0.7087 (m-80) cc_final: 0.6769 (m-80) REVERT: C 221 LYS cc_start: 0.7269 (mttm) cc_final: 0.6737 (mmtp) REVERT: C 289 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7558 (mp0) REVERT: C 308 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7569 (tp) REVERT: C 309 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7352 (mm-30) REVERT: C 392 ARG cc_start: 0.6576 (ttt90) cc_final: 0.6223 (ttp-170) REVERT: C 595 ASP cc_start: 0.5811 (m-30) cc_final: 0.5160 (t0) REVERT: C 647 GLU cc_start: 0.7070 (tt0) cc_final: 0.6723 (pt0) REVERT: C 679 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6394 (mtm110) REVERT: C 687 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6709 (mtm-85) REVERT: C 709 GLU cc_start: 0.7450 (tt0) cc_final: 0.6131 (mt-10) REVERT: D 122 MET cc_start: 0.6682 (mtt) cc_final: 0.6482 (mtp) REVERT: D 133 ASN cc_start: 0.8023 (t0) cc_final: 0.7810 (t0) REVERT: D 161 PHE cc_start: 0.7084 (m-80) cc_final: 0.6769 (m-80) REVERT: D 221 LYS cc_start: 0.7289 (mttm) cc_final: 0.6756 (mmtp) REVERT: D 289 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7553 (mp0) REVERT: D 308 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7563 (tp) REVERT: D 309 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7337 (mm-30) REVERT: D 392 ARG cc_start: 0.6594 (ttt90) cc_final: 0.6237 (ttp-170) REVERT: D 595 ASP cc_start: 0.5805 (m-30) cc_final: 0.5153 (t0) REVERT: D 647 GLU cc_start: 0.7055 (tt0) cc_final: 0.6705 (pt0) REVERT: D 679 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6404 (mtm110) REVERT: D 687 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6737 (mtm-85) REVERT: D 709 GLU cc_start: 0.7460 (tt0) cc_final: 0.6136 (mt-10) outliers start: 44 outliers final: 24 residues processed: 274 average time/residue: 1.1913 time to fit residues: 371.8123 Evaluate side-chains 268 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 534 LEU Chi-restraints excluded: chain D residue 621 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 221 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 161 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 = 0.3846 r_free = 0.3846 target = 0.161711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122140 restraints weight = 22796.366| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.29 r_work: 0.3342 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20220 Z= 0.101 Angle : 0.446 6.174 27404 Z= 0.230 Chirality : 0.037 0.143 3100 Planarity : 0.003 0.041 3348 Dihedral : 7.773 57.944 2852 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.17), residues: 2392 helix: 1.93 (0.13), residues: 1484 sheet: 0.10 (0.52), residues: 100 loop : 0.10 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 333 HIS 0.003 0.001 HIS D 251 PHE 0.019 0.001 PHE D 405 TYR 0.006 0.001 TYR D 525 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.02821 ( 1108) hydrogen bonds : angle 3.84089 ( 3168) covalent geometry : bond 0.00240 (20220) covalent geometry : angle 0.44581 (27404) *********************** 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 292 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 2.043 Fit side-chains REVERT: A 122 MET cc_start: 0.6750 (mtt) cc_final: 0.6521 (mtp) REVERT: A 161 PHE cc_start: 0.7072 (m-80) cc_final: 0.6809 (m-80) REVERT: A 221 LYS cc_start: 0.7275 (mttm) cc_final: 0.6769 (mmtp) REVERT: A 289 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7537 (mp0) REVERT: A 308 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7538 (tp) REVERT: A 309 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 392 ARG cc_start: 0.6554 (ttt90) cc_final: 0.6217 (ttp-170) REVERT: A 595 ASP cc_start: 0.5829 (m-30) cc_final: 0.5184 (t0) REVERT: A 641 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6465 (mp) REVERT: A 647 GLU cc_start: 0.7106 (tt0) cc_final: 0.6733 (pt0) REVERT: A 679 ARG cc_start: 0.7116 (mtt180) cc_final: 0.6449 (mtm110) REVERT: A 687 ARG cc_start: 0.7350 (mtt180) cc_final: 0.6764 (mtm-85) REVERT: A 709 GLU cc_start: 0.7446 (tt0) cc_final: 0.6133 (mp0) REVERT: B 161 PHE cc_start: 0.7057 (m-80) cc_final: 0.6802 (m-80) REVERT: B 221 LYS cc_start: 0.7263 (mttm) cc_final: 0.6753 (mmtp) REVERT: B 289 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7536 (mp0) REVERT: B 308 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7537 (tp) REVERT: B 309 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7335 (mm-30) REVERT: B 392 ARG cc_start: 0.6569 (ttt90) cc_final: 0.6233 (ttp-170) REVERT: B 595 ASP cc_start: 0.5789 (m-30) cc_final: 0.5151 (t0) REVERT: B 641 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6472 (mp) REVERT: B 647 GLU cc_start: 0.7100 (tt0) cc_final: 0.6733 (pt0) REVERT: B 679 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6426 (mtm110) REVERT: B 687 ARG cc_start: 0.7356 (mtt180) cc_final: 0.6764 (mtm-85) REVERT: B 709 GLU cc_start: 0.7460 (tt0) cc_final: 0.6152 (mp0) REVERT: C 161 PHE cc_start: 0.7096 (m-80) cc_final: 0.6821 (m-80) REVERT: C 221 LYS cc_start: 0.7258 (mttm) cc_final: 0.6752 (mmtp) REVERT: C 289 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7518 (mp0) REVERT: C 308 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7547 (tp) REVERT: C 309 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7353 (mm-30) REVERT: C 392 ARG cc_start: 0.6550 (ttt90) cc_final: 0.6212 (ttp-170) REVERT: C 595 ASP cc_start: 0.5784 (m-30) cc_final: 0.5144 (t0) REVERT: C 641 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6477 (mp) REVERT: C 647 GLU cc_start: 0.7084 (tt0) cc_final: 0.6710 (pt0) REVERT: C 679 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6437 (mtm110) REVERT: C 687 ARG cc_start: 0.7351 (mtt180) cc_final: 0.6758 (mtm-85) REVERT: C 709 GLU cc_start: 0.7469 (tt0) cc_final: 0.6162 (mp0) REVERT: D 122 MET cc_start: 0.6711 (mtt) cc_final: 0.6500 (mtp) REVERT: D 161 PHE cc_start: 0.7114 (m-80) cc_final: 0.6841 (m-80) REVERT: D 221 LYS cc_start: 0.7268 (mttm) cc_final: 0.6762 (mmtp) REVERT: D 289 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7544 (mp0) REVERT: D 308 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7541 (tp) REVERT: D 309 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7346 (mm-30) REVERT: D 392 ARG cc_start: 0.6558 (ttt90) cc_final: 0.6221 (ttp-170) REVERT: D 595 ASP cc_start: 0.5750 (m-30) cc_final: 0.5115 (t0) REVERT: D 641 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6442 (mp) REVERT: D 647 GLU cc_start: 0.7080 (tt0) cc_final: 0.6707 (pt0) REVERT: D 679 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6461 (mtm110) REVERT: D 687 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6775 (mtm-85) REVERT: D 709 GLU cc_start: 0.7460 (tt0) cc_final: 0.6143 (mp0) outliers start: 39 outliers final: 24 residues processed: 271 average time/residue: 1.1098 time to fit residues: 345.2358 Evaluate side-chains 274 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 A residue 641 LEU 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 B residue 641 LEU 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 C residue 641 LEU 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 534 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 0.0370 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- 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 = 0.160836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121086 restraints weight = 22769.601| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.34 r_work: 0.3330 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20220 Z= 0.115 Angle : 0.474 8.925 27404 Z= 0.241 Chirality : 0.038 0.131 3100 Planarity : 0.003 0.041 3348 Dihedral : 7.827 60.275 2852 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.91 % Allowed : 12.69 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.17), residues: 2392 helix: 1.91 (0.13), residues: 1484 sheet: 0.13 (0.51), residues: 100 loop : 0.09 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 333 HIS 0.003 0.001 HIS B 313 PHE 0.020 0.001 PHE B 405 TYR 0.006 0.001 TYR D 228 ARG 0.002 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 1108) hydrogen bonds : angle 3.85842 ( 3168) covalent geometry : bond 0.00278 (20220) covalent geometry : angle 0.47406 (27404) *********************** 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 291 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 251 time to evaluate : 2.309 Fit side-chains REVERT: A 122 MET cc_start: 0.6798 (mtt) cc_final: 0.6539 (mtp) REVERT: A 161 PHE cc_start: 0.7090 (m-80) cc_final: 0.6811 (m-80) REVERT: A 221 LYS cc_start: 0.7278 (mttm) cc_final: 0.6773 (mmtp) REVERT: A 289 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7523 (mp0) REVERT: A 308 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7566 (tp) REVERT: A 309 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 392 ARG cc_start: 0.6573 (ttt90) cc_final: 0.6233 (ttp-170) REVERT: A 433 MET cc_start: 0.6500 (mmp) cc_final: 0.5554 (ttp) REVERT: A 595 ASP cc_start: 0.5844 (m-30) cc_final: 0.5196 (t0) REVERT: A 647 GLU cc_start: 0.7064 (tt0) cc_final: 0.6560 (pt0) REVERT: A 679 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6407 (mtm110) REVERT: A 687 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6711 (mtm-85) REVERT: A 709 GLU cc_start: 0.7495 (tt0) cc_final: 0.6181 (mt-10) REVERT: B 161 PHE cc_start: 0.7059 (m-80) cc_final: 0.6792 (m-80) REVERT: B 221 LYS cc_start: 0.7245 (mttm) cc_final: 0.6709 (mmtp) REVERT: B 289 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7523 (mp0) REVERT: B 308 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7549 (tp) REVERT: B 309 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 392 ARG cc_start: 0.6568 (ttt90) cc_final: 0.6230 (ttp-170) REVERT: B 433 MET cc_start: 0.6537 (mmp) cc_final: 0.5583 (ttp) REVERT: B 595 ASP cc_start: 0.5801 (m-30) cc_final: 0.5159 (t0) REVERT: B 647 GLU cc_start: 0.7065 (tt0) cc_final: 0.6565 (pt0) REVERT: B 679 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6423 (mtm110) REVERT: B 687 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6720 (mtm-85) REVERT: B 709 GLU cc_start: 0.7475 (tt0) cc_final: 0.6164 (mt-10) REVERT: C 161 PHE cc_start: 0.7076 (m-80) cc_final: 0.6792 (m-80) REVERT: C 221 LYS cc_start: 0.7264 (mttm) cc_final: 0.6757 (mmtp) REVERT: C 289 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7503 (mp0) REVERT: C 308 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7568 (tp) REVERT: C 309 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7366 (mm-30) REVERT: C 392 ARG cc_start: 0.6561 (ttt90) cc_final: 0.6222 (ttp-170) REVERT: C 433 MET cc_start: 0.6516 (mmp) cc_final: 0.5564 (ttp) REVERT: C 595 ASP cc_start: 0.5793 (m-30) cc_final: 0.5151 (t0) REVERT: C 647 GLU cc_start: 0.7057 (tt0) cc_final: 0.6555 (pt0) REVERT: C 679 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6432 (mtm110) REVERT: C 687 ARG cc_start: 0.7304 (mtt180) cc_final: 0.6710 (mtm-85) REVERT: C 709 GLU cc_start: 0.7480 (tt0) cc_final: 0.6173 (mt-10) REVERT: D 122 MET cc_start: 0.6782 (mtt) cc_final: 0.6526 (mtp) REVERT: D 161 PHE cc_start: 0.7115 (m-80) cc_final: 0.6837 (m-80) REVERT: D 221 LYS cc_start: 0.7268 (mttm) cc_final: 0.6762 (mmtp) REVERT: D 289 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7533 (mp0) REVERT: D 308 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7564 (tp) REVERT: D 309 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 392 ARG cc_start: 0.6568 (ttt90) cc_final: 0.6229 (ttp-170) REVERT: D 433 MET cc_start: 0.6517 (mmp) cc_final: 0.5848 (mmm) REVERT: D 595 ASP cc_start: 0.5777 (m-30) cc_final: 0.5137 (t0) REVERT: D 647 GLU cc_start: 0.7055 (tt0) cc_final: 0.6551 (pt0) REVERT: D 679 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6445 (mtm110) REVERT: D 687 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6732 (mtm-85) REVERT: D 709 GLU cc_start: 0.7464 (tt0) cc_final: 0.6153 (mt-10) outliers start: 40 outliers final: 24 residues processed: 271 average time/residue: 1.1243 time to fit residues: 351.4395 Evaluate side-chains 262 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 461 LEU 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 96 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 145 optimal weight: 0.0170 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 0.0050 chunk 200 optimal weight: 1.9990 overall best weight: 0.5434 ------------------------------------------------------------------------------- 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 = 0.162074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122763 restraints weight = 22727.569| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.28 r_work: 0.3352 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20220 Z= 0.097 Angle : 0.464 8.862 27404 Z= 0.234 Chirality : 0.037 0.171 3100 Planarity : 0.003 0.041 3348 Dihedral : 7.688 57.804 2852 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.72 % Allowed : 13.31 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2392 helix: 2.00 (0.13), residues: 1484 sheet: 0.11 (0.51), residues: 100 loop : 0.12 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 333 HIS 0.003 0.001 HIS B 251 PHE 0.021 0.001 PHE D 405 TYR 0.006 0.001 TYR B 544 ARG 0.004 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.02761 ( 1108) hydrogen bonds : angle 3.81417 ( 3168) covalent geometry : bond 0.00227 (20220) covalent geometry : angle 0.46396 (27404) ********************** 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 284 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 2.011 Fit side-chains REVERT: A 91 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7056 (mp0) REVERT: A 122 MET cc_start: 0.6749 (mtt) cc_final: 0.6507 (mtp) REVERT: A 161 PHE cc_start: 0.7102 (m-80) cc_final: 0.6830 (m-80) REVERT: A 178 GLN cc_start: 0.7480 (mt0) cc_final: 0.7257 (pm20) REVERT: A 221 LYS cc_start: 0.7268 (mttm) cc_final: 0.6772 (mmtp) REVERT: A 289 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7490 (mp0) REVERT: A 308 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7493 (tp) REVERT: A 309 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 392 ARG cc_start: 0.6571 (ttt90) cc_final: 0.6239 (ttp-170) REVERT: A 433 MET cc_start: 0.6512 (mmp) cc_final: 0.5833 (mmm) REVERT: A 595 ASP cc_start: 0.5816 (m-30) cc_final: 0.5188 (t0) REVERT: A 647 GLU cc_start: 0.7073 (tt0) cc_final: 0.6572 (pt0) REVERT: A 679 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6526 (mtm110) REVERT: A 687 ARG cc_start: 0.7264 (mtt180) cc_final: 0.6703 (mtm-85) REVERT: A 709 GLU cc_start: 0.7484 (tt0) cc_final: 0.6177 (mt-10) REVERT: B 91 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7057 (mp0) REVERT: B 161 PHE cc_start: 0.7028 (m-80) cc_final: 0.6774 (m-80) REVERT: B 178 GLN cc_start: 0.7467 (mt0) cc_final: 0.7241 (pm20) REVERT: B 221 LYS cc_start: 0.7263 (mttm) cc_final: 0.6765 (mmtp) REVERT: B 289 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7507 (mp0) REVERT: B 308 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7473 (tp) REVERT: B 309 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 392 ARG cc_start: 0.6587 (ttt90) cc_final: 0.6256 (ttp-170) REVERT: B 433 MET cc_start: 0.6551 (mmp) cc_final: 0.5868 (mmm) REVERT: B 595 ASP cc_start: 0.5788 (m-30) cc_final: 0.5165 (t0) REVERT: B 647 GLU cc_start: 0.7077 (tt0) cc_final: 0.6579 (pt0) REVERT: B 679 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6487 (mtm110) REVERT: B 687 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6723 (mtm-85) REVERT: B 709 GLU cc_start: 0.7464 (tt0) cc_final: 0.6166 (mt-10) REVERT: C 91 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7063 (mp0) REVERT: C 161 PHE cc_start: 0.7098 (m-80) cc_final: 0.6828 (m-80) REVERT: C 178 GLN cc_start: 0.7460 (mt0) cc_final: 0.7237 (pm20) REVERT: C 221 LYS cc_start: 0.7259 (mttm) cc_final: 0.6762 (mmtp) REVERT: C 289 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7514 (mp0) REVERT: C 308 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7492 (tp) REVERT: C 309 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7358 (mm-30) REVERT: C 392 ARG cc_start: 0.6571 (ttt90) cc_final: 0.6236 (ttp-170) REVERT: C 433 MET cc_start: 0.6523 (mmp) cc_final: 0.5843 (mmm) REVERT: C 595 ASP cc_start: 0.5767 (m-30) cc_final: 0.5148 (t0) REVERT: C 647 GLU cc_start: 0.7075 (tt0) cc_final: 0.6571 (pt0) REVERT: C 679 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6500 (mtm110) REVERT: C 687 ARG cc_start: 0.7283 (mtt180) cc_final: 0.6710 (mtm-85) REVERT: C 709 GLU cc_start: 0.7475 (tt0) cc_final: 0.6178 (mt-10) REVERT: D 91 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7058 (mp0) REVERT: D 122 MET cc_start: 0.6790 (mtt) cc_final: 0.6532 (mtp) REVERT: D 161 PHE cc_start: 0.7121 (m-80) cc_final: 0.6858 (m-80) REVERT: D 178 GLN cc_start: 0.7487 (mt0) cc_final: 0.7265 (pm20) REVERT: D 221 LYS cc_start: 0.7263 (mttm) cc_final: 0.6766 (mmtp) REVERT: D 289 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7497 (mp0) REVERT: D 308 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7487 (tp) REVERT: D 309 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7354 (mm-30) REVERT: D 392 ARG cc_start: 0.6580 (ttt90) cc_final: 0.6244 (ttp-170) REVERT: D 433 MET cc_start: 0.6524 (mmp) cc_final: 0.5842 (mmm) REVERT: D 595 ASP cc_start: 0.5767 (m-30) cc_final: 0.5146 (t0) REVERT: D 647 GLU cc_start: 0.7076 (tt0) cc_final: 0.6575 (pt0) REVERT: D 679 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6505 (mtm110) REVERT: D 687 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6727 (mtm-85) REVERT: D 709 GLU cc_start: 0.7451 (tt0) cc_final: 0.6153 (mt-10) outliers start: 36 outliers final: 24 residues processed: 267 average time/residue: 1.2088 time to fit residues: 367.6604 Evaluate side-chains 267 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 528 MET 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 528 MET 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 528 MET 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 528 MET 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 136 optimal weight: 0.5980 chunk 228 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 196 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 217 optimal weight: 0.0020 chunk 134 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.4306 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.163434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124276 restraints weight = 22852.301| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.29 r_work: 0.3373 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20220 Z= 0.088 Angle : 0.443 8.741 27404 Z= 0.226 Chirality : 0.037 0.134 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.508 58.928 2852 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.48 % Allowed : 13.31 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.17), residues: 2392 helix: 2.08 (0.14), residues: 1488 sheet: 0.16 (0.52), residues: 100 loop : 0.11 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 333 HIS 0.002 0.001 HIS A 165 PHE 0.023 0.001 PHE C 405 TYR 0.006 0.001 TYR D 544 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.02591 ( 1108) hydrogen bonds : angle 3.73971 ( 3168) covalent geometry : bond 0.00203 (20220) covalent geometry : angle 0.44282 (27404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14530.75 seconds wall clock time: 250 minutes 16.34 seconds (15016.34 seconds total)