Starting phenix.real_space_refine on Tue Jun 17 07:42:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3y_44160/06_2025/9b3y_44160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3y_44160/06_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_44160/06_2025/9b3y_44160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3y_44160/06_2025/9b3y_44160.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3y_44160/06_2025/9b3y_44160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3y_44160/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.16, per 1000 atoms: 0.57 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: 5.18 Conformation dependent library (CDL) restraints added in 2.7 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: 2.37 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: 6.08 Time building geometry restraints manager: 6.01 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: 0.14 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: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.850 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.760 ------------------------------------------------------------------------------- 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 : 2.766 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: 1.3940 time to fit residues: 611.9953 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 : 2.404 ------------------------------------------------------------------------------- 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 = 0.161304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122863 restraints weight = 22504.700| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.20 r_work: 0.3346 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 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 74.956 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 4.33445 ( 3168) covalent geometry : bond 0.00308 (20220) covalent geometry : angle 0.54818 (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 : 2.286 Fit side-chains REVERT: A 108 ASP cc_start: 0.6375 (m-30) cc_final: 0.5980 (p0) REVERT: A 151 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6585 (tt) REVERT: A 161 PHE cc_start: 0.6929 (m-80) cc_final: 0.6224 (m-80) REVERT: A 197 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7390 (tpt-90) REVERT: A 221 LYS cc_start: 0.7322 (mttm) cc_final: 0.6852 (mmtp) REVERT: A 240 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 277 MET cc_start: 0.6542 (mtp) cc_final: 0.6295 (mtp) REVERT: A 289 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7523 (mp0) REVERT: A 392 ARG cc_start: 0.6595 (ttt90) cc_final: 0.6214 (ttp-170) REVERT: A 530 GLN cc_start: 0.6259 (pt0) cc_final: 0.4800 (tp-100) REVERT: A 595 ASP cc_start: 0.5532 (m-30) cc_final: 0.4989 (t0) REVERT: A 645 MET cc_start: 0.7454 (mtt) cc_final: 0.7222 (mtp) REVERT: A 679 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6294 (mtm110) REVERT: A 687 ARG cc_start: 0.7467 (mtt180) cc_final: 0.6692 (mtm-85) REVERT: A 701 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7872 (mm-30) REVERT: B 108 ASP cc_start: 0.6377 (m-30) cc_final: 0.5976 (p0) REVERT: B 151 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6591 (tt) REVERT: B 161 PHE cc_start: 0.6926 (m-80) cc_final: 0.6216 (m-80) REVERT: B 197 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7381 (tpt-90) REVERT: B 221 LYS cc_start: 0.7345 (mttm) cc_final: 0.6879 (mmtp) REVERT: B 240 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 277 MET cc_start: 0.6530 (mtp) cc_final: 0.6285 (mtp) REVERT: B 289 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7531 (mp0) REVERT: B 392 ARG cc_start: 0.6590 (ttt90) cc_final: 0.6207 (ttp-170) REVERT: B 530 GLN cc_start: 0.6269 (pt0) cc_final: 0.4815 (tp-100) REVERT: B 595 ASP cc_start: 0.5507 (m-30) cc_final: 0.4965 (t0) REVERT: B 645 MET cc_start: 0.7440 (mtt) cc_final: 0.7210 (mtp) REVERT: B 679 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6318 (mtm110) REVERT: B 687 ARG cc_start: 0.7440 (mtt180) cc_final: 0.6652 (mtm-85) REVERT: B 701 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7872 (mm-30) REVERT: C 108 ASP cc_start: 0.6380 (m-30) cc_final: 0.5981 (p0) REVERT: C 151 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6590 (tt) REVERT: C 161 PHE cc_start: 0.6920 (m-80) cc_final: 0.6213 (m-80) REVERT: C 197 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7414 (tpt-90) REVERT: C 221 LYS cc_start: 0.7325 (mttm) cc_final: 0.6856 (mmtp) REVERT: C 240 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7664 (mt-10) REVERT: C 277 MET cc_start: 0.6560 (mtp) cc_final: 0.6311 (mtp) REVERT: C 289 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7539 (mp0) REVERT: C 392 ARG cc_start: 0.6597 (ttt90) cc_final: 0.6213 (ttp-170) REVERT: C 530 GLN cc_start: 0.6265 (pt0) cc_final: 0.4811 (tp-100) REVERT: C 595 ASP cc_start: 0.5522 (m-30) cc_final: 0.4978 (t0) REVERT: C 645 MET cc_start: 0.7468 (mtt) cc_final: 0.7233 (mtp) REVERT: C 679 ARG cc_start: 0.7129 (mtt180) cc_final: 0.6318 (mtm110) REVERT: C 687 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6690 (mtm-85) REVERT: C 701 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7880 (mm-30) REVERT: D 108 ASP cc_start: 0.6374 (m-30) cc_final: 0.5976 (p0) REVERT: D 151 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6576 (tt) REVERT: D 161 PHE cc_start: 0.6933 (m-80) cc_final: 0.6217 (m-80) REVERT: D 197 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7413 (tpt-90) REVERT: D 221 LYS cc_start: 0.7336 (mttm) cc_final: 0.6866 (mmtp) REVERT: D 240 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 277 MET cc_start: 0.6555 (mtp) cc_final: 0.6305 (mtp) REVERT: D 289 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7525 (mp0) REVERT: D 392 ARG cc_start: 0.6616 (ttt90) cc_final: 0.6235 (ttp-170) REVERT: D 530 GLN cc_start: 0.6265 (pt0) cc_final: 0.4804 (tp-100) REVERT: D 595 ASP cc_start: 0.5556 (m-30) cc_final: 0.5006 (t0) REVERT: D 645 MET cc_start: 0.7493 (mtt) cc_final: 0.7259 (mtp) REVERT: D 679 ARG cc_start: 0.7111 (mtt180) cc_final: 0.6311 (mtm110) REVERT: D 687 ARG cc_start: 0.7476 (mtt180) cc_final: 0.6685 (mtm-85) REVERT: D 701 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7869 (mm-30) outliers start: 30 outliers final: 0 residues processed: 331 average time/residue: 1.2739 time to fit residues: 478.5709 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 : 2.288 ------------------------------------------------------------------------------- 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: 0.0970 chunk 206 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 198 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 160 optimal weight: 0.4980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.163159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.125280 restraints weight = 22499.277| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.19 r_work: 0.3372 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20220 Z= 0.098 Angle : 0.458 6.678 27404 Z= 0.246 Chirality : 0.038 0.146 3100 Planarity : 0.004 0.040 3348 Dihedral : 8.880 59.547 2868 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.62 % Allowed : 10.07 % Favored : 88.31 % 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: 1.62 (0.17), residues: 2392 helix: 1.59 (0.13), residues: 1492 sheet: 0.06 (0.50), residues: 116 loop : 0.39 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 333 HIS 0.004 0.001 HIS C 251 PHE 0.015 0.001 PHE C 467 TYR 0.010 0.001 TYR A 525 ARG 0.006 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 1108) hydrogen bonds : angle 4.06609 ( 3168) covalent geometry : bond 0.00225 (20220) covalent geometry : angle 0.45780 (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 298 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 2.253 Fit side-chains REVERT: A 151 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6760 (tt) REVERT: A 161 PHE cc_start: 0.7015 (m-80) cc_final: 0.6540 (m-80) REVERT: A 221 LYS cc_start: 0.7295 (mttm) cc_final: 0.6921 (mmtp) REVERT: A 240 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7607 (mt-10) REVERT: A 277 MET cc_start: 0.6617 (mtp) cc_final: 0.6323 (mtp) REVERT: A 289 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7550 (mp0) REVERT: A 309 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 392 ARG cc_start: 0.6619 (ttt90) cc_final: 0.6200 (ttp-170) REVERT: A 530 GLN cc_start: 0.6118 (pt0) cc_final: 0.4780 (mm-40) REVERT: A 595 ASP cc_start: 0.5681 (m-30) cc_final: 0.5094 (t0) REVERT: A 679 ARG cc_start: 0.7084 (mtt180) cc_final: 0.6311 (mtm110) REVERT: A 687 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6689 (mtm-85) REVERT: A 701 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7851 (mm-30) REVERT: A 709 GLU cc_start: 0.7481 (tt0) cc_final: 0.6147 (mt-10) REVERT: B 151 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6750 (tt) REVERT: B 161 PHE cc_start: 0.6996 (m-80) cc_final: 0.6508 (m-80) REVERT: B 221 LYS cc_start: 0.7303 (mttm) cc_final: 0.6929 (mmtp) REVERT: B 240 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 277 MET cc_start: 0.6579 (mtp) cc_final: 0.6285 (mtp) REVERT: B 289 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7556 (mp0) REVERT: B 309 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 392 ARG cc_start: 0.6612 (ttt90) cc_final: 0.6196 (ttp-170) REVERT: B 530 GLN cc_start: 0.6115 (pt0) cc_final: 0.4773 (mm-40) REVERT: B 595 ASP cc_start: 0.5674 (m-30) cc_final: 0.5088 (t0) REVERT: B 679 ARG cc_start: 0.7131 (mtt180) cc_final: 0.6345 (mtm110) REVERT: B 687 ARG cc_start: 0.7406 (mtt180) cc_final: 0.6663 (mtm-85) REVERT: B 701 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7847 (mm-30) REVERT: B 709 GLU cc_start: 0.7509 (tt0) cc_final: 0.6174 (mt-10) REVERT: C 151 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6697 (tt) REVERT: C 161 PHE cc_start: 0.7029 (m-80) cc_final: 0.6548 (m-80) REVERT: C 221 LYS cc_start: 0.7324 (mttm) cc_final: 0.6953 (mmtp) REVERT: C 240 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 277 MET cc_start: 0.6642 (mtp) cc_final: 0.6348 (mtp) REVERT: C 289 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7567 (mp0) REVERT: C 309 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 392 ARG cc_start: 0.6584 (ttt90) cc_final: 0.6165 (ttp-170) REVERT: C 530 GLN cc_start: 0.6108 (pt0) cc_final: 0.4765 (mm-40) REVERT: C 595 ASP cc_start: 0.5667 (m-30) cc_final: 0.5081 (t0) REVERT: C 679 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6343 (mtm110) REVERT: C 687 ARG cc_start: 0.7420 (mtt180) cc_final: 0.6674 (mtm-85) REVERT: C 701 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7847 (mm-30) REVERT: C 709 GLU cc_start: 0.7475 (tt0) cc_final: 0.6143 (mt-10) REVERT: D 151 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6741 (tt) REVERT: D 161 PHE cc_start: 0.7007 (m-80) cc_final: 0.6527 (m-80) REVERT: D 221 LYS cc_start: 0.7328 (mttm) cc_final: 0.6958 (mmtp) REVERT: D 240 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 277 MET cc_start: 0.6599 (mtp) cc_final: 0.6304 (mtp) REVERT: D 289 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7567 (mp0) REVERT: D 309 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7385 (mm-30) REVERT: D 392 ARG cc_start: 0.6625 (ttt90) cc_final: 0.6209 (ttp-170) REVERT: D 530 GLN cc_start: 0.6095 (pt0) cc_final: 0.4755 (mm-40) REVERT: D 595 ASP cc_start: 0.5644 (m-30) cc_final: 0.5062 (t0) REVERT: D 679 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6355 (mtm110) REVERT: D 687 ARG cc_start: 0.7418 (mtt180) cc_final: 0.6669 (mtm-85) REVERT: D 701 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7843 (mm-30) REVERT: D 709 GLU cc_start: 0.7508 (tt0) cc_final: 0.6175 (mt-10) outliers start: 34 outliers final: 8 residues processed: 282 average time/residue: 1.1977 time to fit residues: 386.7234 Evaluate side-chains 248 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 236 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 119 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: 0.0770 chunk 66 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 201 optimal weight: 0.1980 chunk 123 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 161 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.163994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125561 restraints weight = 22841.936| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.24 r_work: 0.3383 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2785 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= 0.089 Angle : 0.429 4.994 27404 Z= 0.228 Chirality : 0.037 0.178 3100 Planarity : 0.003 0.039 3348 Dihedral : 8.021 57.702 2852 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.91 % Allowed : 10.88 % Favored : 87.21 % 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: 1.97 (0.17), residues: 2392 helix: 1.86 (0.13), residues: 1512 sheet: 0.97 (0.53), residues: 96 loop : 0.40 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 333 HIS 0.003 0.001 HIS C 251 PHE 0.013 0.001 PHE D 405 TYR 0.008 0.001 TYR C 525 ARG 0.005 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.02777 ( 1108) hydrogen bonds : angle 3.90815 ( 3168) covalent geometry : bond 0.00200 (20220) covalent geometry : angle 0.42857 (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 320 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 2.179 Fit side-chains REVERT: A 161 PHE cc_start: 0.6929 (m-80) cc_final: 0.6540 (m-80) REVERT: A 221 LYS cc_start: 0.7247 (mttm) cc_final: 0.6723 (mmtp) REVERT: A 240 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 277 MET cc_start: 0.6570 (mtp) cc_final: 0.6237 (mtp) REVERT: A 289 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7530 (mp0) REVERT: A 309 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 392 ARG cc_start: 0.6510 (ttt90) cc_final: 0.6141 (ttp-170) REVERT: A 595 ASP cc_start: 0.5686 (m-30) cc_final: 0.5114 (t0) REVERT: A 679 ARG cc_start: 0.7043 (mtt180) cc_final: 0.6251 (mtm110) REVERT: A 687 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6820 (mtm-85) REVERT: A 701 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7810 (mm-30) REVERT: A 709 GLU cc_start: 0.7366 (tt0) cc_final: 0.6211 (mt-10) REVERT: B 161 PHE cc_start: 0.6913 (m-80) cc_final: 0.6517 (m-80) REVERT: B 221 LYS cc_start: 0.7265 (mttm) cc_final: 0.6831 (mmtp) REVERT: B 240 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 277 MET cc_start: 0.6550 (mtp) cc_final: 0.6214 (mtp) REVERT: B 289 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7547 (mp0) REVERT: B 309 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 392 ARG cc_start: 0.6512 (ttt90) cc_final: 0.6153 (ttp-170) REVERT: B 595 ASP cc_start: 0.5661 (m-30) cc_final: 0.5095 (t0) REVERT: B 679 ARG cc_start: 0.7071 (mtt180) cc_final: 0.6279 (mtm110) REVERT: B 687 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6806 (mtm-85) REVERT: B 701 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7808 (mm-30) REVERT: B 709 GLU cc_start: 0.7380 (tt0) cc_final: 0.6225 (mt-10) REVERT: C 161 PHE cc_start: 0.6925 (m-80) cc_final: 0.6536 (m-80) REVERT: C 221 LYS cc_start: 0.7267 (mttm) cc_final: 0.6747 (mmtp) REVERT: C 240 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7633 (mt-10) REVERT: C 277 MET cc_start: 0.6605 (mtp) cc_final: 0.6271 (mtp) REVERT: C 289 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7575 (mp0) REVERT: C 309 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7457 (mm-30) REVERT: C 392 ARG cc_start: 0.6513 (ttt90) cc_final: 0.6151 (ttp-170) REVERT: C 595 ASP cc_start: 0.5644 (m-30) cc_final: 0.5077 (t0) REVERT: C 679 ARG cc_start: 0.7017 (mtt180) cc_final: 0.6230 (mtm110) REVERT: C 687 ARG cc_start: 0.7414 (mtt180) cc_final: 0.6830 (mtm-85) REVERT: C 701 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7826 (mm-30) REVERT: C 709 GLU cc_start: 0.7384 (tt0) cc_final: 0.6227 (mt-10) REVERT: D 161 PHE cc_start: 0.6919 (m-80) cc_final: 0.6525 (m-80) REVERT: D 221 LYS cc_start: 0.7291 (mttm) cc_final: 0.6766 (mmtp) REVERT: D 240 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7647 (mt-10) REVERT: D 277 MET cc_start: 0.6591 (mtp) cc_final: 0.6255 (mtp) REVERT: D 289 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7524 (mp0) REVERT: D 309 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7443 (mm-30) REVERT: D 392 ARG cc_start: 0.6523 (ttt90) cc_final: 0.6162 (ttp-170) REVERT: D 595 ASP cc_start: 0.5640 (m-30) cc_final: 0.5076 (t0) REVERT: D 679 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6244 (mtm110) REVERT: D 687 ARG cc_start: 0.7403 (mtt180) cc_final: 0.6817 (mtm-85) REVERT: D 701 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7818 (mm-30) REVERT: D 709 GLU cc_start: 0.7349 (tt0) cc_final: 0.6176 (mt-10) outliers start: 40 outliers final: 20 residues processed: 296 average time/residue: 1.2917 time to fit residues: 433.7261 Evaluate side-chains 276 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 2.326 ------------------------------------------------------------------------------- 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 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 461 LEU 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 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 461 LEU Chi-restraints excluded: chain D residue 463 ILE 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: 5.9990 chunk 108 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 188 optimal weight: 0.3980 chunk 50 optimal weight: 7.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.156139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116206 restraints weight = 23081.250| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.36 r_work: 0.3271 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20220 Z= 0.245 Angle : 0.602 7.555 27404 Z= 0.303 Chirality : 0.044 0.243 3100 Planarity : 0.004 0.041 3348 Dihedral : 9.145 87.205 2852 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.05 % Allowed : 11.31 % Favored : 86.64 % 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: 1.23 (0.17), residues: 2392 helix: 1.39 (0.13), residues: 1500 sheet: 0.11 (0.52), residues: 100 loop : -0.07 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 333 HIS 0.006 0.002 HIS A 521 PHE 0.018 0.002 PHE C 394 TYR 0.019 0.002 TYR B 228 ARG 0.003 0.001 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 1108) hydrogen bonds : angle 4.22770 ( 3168) covalent geometry : bond 0.00613 (20220) covalent geometry : angle 0.60158 (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 315 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 2.154 Fit side-chains REVERT: A 161 PHE cc_start: 0.7043 (m-80) cc_final: 0.6615 (m-80) REVERT: A 221 LYS cc_start: 0.7293 (mttm) cc_final: 0.6897 (mmtp) REVERT: A 289 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7542 (mp0) REVERT: A 309 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7537 (mm-30) REVERT: A 392 ARG cc_start: 0.6627 (ttt90) cc_final: 0.6234 (ttp-170) REVERT: A 470 SER cc_start: 0.7988 (m) cc_final: 0.7466 (p) REVERT: A 512 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7704 (mm) REVERT: A 530 GLN cc_start: 0.5996 (pt0) cc_final: 0.4820 (tp-100) REVERT: A 595 ASP cc_start: 0.5762 (m-30) cc_final: 0.5057 (t0) REVERT: A 609 GLU cc_start: 0.6726 (mt-10) cc_final: 0.5855 (tp30) REVERT: A 647 GLU cc_start: 0.7059 (tt0) cc_final: 0.6809 (pt0) REVERT: A 679 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6336 (mtm110) REVERT: A 687 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6631 (mtm-85) REVERT: A 709 GLU cc_start: 0.7600 (tt0) cc_final: 0.6225 (mt-10) REVERT: B 161 PHE cc_start: 0.7036 (m-80) cc_final: 0.6609 (m-80) REVERT: B 221 LYS cc_start: 0.7281 (mttm) cc_final: 0.6882 (mmtp) REVERT: B 289 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7557 (mp0) REVERT: B 309 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7532 (mm-30) REVERT: B 392 ARG cc_start: 0.6628 (ttt90) cc_final: 0.6237 (ttp-170) REVERT: B 470 SER cc_start: 0.7992 (m) cc_final: 0.7466 (p) REVERT: B 512 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7734 (mm) REVERT: B 530 GLN cc_start: 0.5987 (pt0) cc_final: 0.4818 (tp-100) REVERT: B 595 ASP cc_start: 0.5727 (m-30) cc_final: 0.5028 (t0) REVERT: B 609 GLU cc_start: 0.6726 (mt-10) cc_final: 0.5853 (tp30) REVERT: B 641 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6705 (mp) REVERT: B 647 GLU cc_start: 0.7051 (tt0) cc_final: 0.6800 (pt0) REVERT: B 679 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6326 (mtm110) REVERT: B 687 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6641 (mtm-85) REVERT: B 709 GLU cc_start: 0.7616 (tt0) cc_final: 0.6245 (mt-10) REVERT: C 161 PHE cc_start: 0.7018 (m-80) cc_final: 0.6594 (m-80) REVERT: C 221 LYS cc_start: 0.7289 (mttm) cc_final: 0.6892 (mmtp) REVERT: C 289 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7571 (mp0) REVERT: C 309 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7548 (mm-30) REVERT: C 392 ARG cc_start: 0.6617 (ttt90) cc_final: 0.6222 (ttp-170) REVERT: C 470 SER cc_start: 0.8002 (m) cc_final: 0.7478 (p) REVERT: C 512 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7744 (mm) REVERT: C 530 GLN cc_start: 0.6002 (pt0) cc_final: 0.4824 (tp-100) REVERT: C 595 ASP cc_start: 0.5720 (m-30) cc_final: 0.5024 (t0) REVERT: C 609 GLU cc_start: 0.6728 (mt-10) cc_final: 0.5861 (tp30) REVERT: C 641 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6741 (mp) REVERT: C 647 GLU cc_start: 0.7054 (tt0) cc_final: 0.6805 (pt0) REVERT: C 679 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6337 (mtm110) REVERT: C 687 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6647 (mtm-85) REVERT: C 709 GLU cc_start: 0.7579 (tt0) cc_final: 0.6200 (mt-10) REVERT: D 161 PHE cc_start: 0.7014 (m-80) cc_final: 0.6586 (m-80) REVERT: D 221 LYS cc_start: 0.7324 (mttm) cc_final: 0.6927 (mmtp) REVERT: D 289 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7546 (mp0) REVERT: D 309 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7542 (mm-30) REVERT: D 392 ARG cc_start: 0.6617 (ttt90) cc_final: 0.6223 (ttp-170) REVERT: D 470 SER cc_start: 0.7987 (m) cc_final: 0.7473 (p) REVERT: D 512 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7713 (mm) REVERT: D 530 GLN cc_start: 0.6008 (pt0) cc_final: 0.4826 (tp-100) REVERT: D 595 ASP cc_start: 0.5719 (m-30) cc_final: 0.5022 (t0) REVERT: D 609 GLU cc_start: 0.6721 (mt-10) cc_final: 0.5850 (tp30) REVERT: D 641 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6747 (mp) REVERT: D 647 GLU cc_start: 0.7043 (tt0) cc_final: 0.6800 (pt0) REVERT: D 679 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6333 (mtm110) REVERT: D 687 ARG cc_start: 0.7403 (mtt180) cc_final: 0.6656 (mtm-85) REVERT: D 709 GLU cc_start: 0.7592 (tt0) cc_final: 0.6216 (mt-10) outliers start: 43 outliers final: 16 residues processed: 292 average time/residue: 1.2971 time to fit residues: 428.3253 Evaluate side-chains 260 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 2.371 ------------------------------------------------------------------------------- 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 512 LEU 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 512 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 534 LEU 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 512 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 534 LEU 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 512 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 85 optimal weight: 0.6980 chunk 148 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 223 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.160462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121770 restraints weight = 22905.290| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.3335 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20220 Z= 0.106 Angle : 0.456 5.615 27404 Z= 0.237 Chirality : 0.038 0.155 3100 Planarity : 0.003 0.040 3348 Dihedral : 8.173 67.318 2852 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.67 % Allowed : 12.07 % 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: 1.67 (0.17), residues: 2392 helix: 1.76 (0.13), residues: 1512 sheet: 0.26 (0.54), residues: 100 loop : 0.05 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 333 HIS 0.003 0.001 HIS C 165 PHE 0.015 0.001 PHE C 467 TYR 0.011 0.001 TYR B 228 ARG 0.003 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 1108) hydrogen bonds : angle 3.95057 ( 3168) covalent geometry : bond 0.00249 (20220) covalent geometry : angle 0.45628 (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 274 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 239 time to evaluate : 2.122 Fit side-chains REVERT: A 161 PHE cc_start: 0.7077 (m-80) cc_final: 0.6722 (m-80) REVERT: A 193 ARG cc_start: 0.8172 (mtp180) cc_final: 0.7942 (mtp85) REVERT: A 221 LYS cc_start: 0.7307 (mttm) cc_final: 0.6938 (mmtp) REVERT: A 289 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7519 (mp0) REVERT: A 309 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 392 ARG cc_start: 0.6563 (ttt90) cc_final: 0.6198 (ttp-170) REVERT: A 595 ASP cc_start: 0.5937 (m-30) cc_final: 0.5246 (t0) REVERT: A 613 GLN cc_start: 0.6710 (mm-40) cc_final: 0.5454 (mp10) REVERT: A 647 GLU cc_start: 0.7240 (tt0) cc_final: 0.6971 (pt0) REVERT: A 679 ARG cc_start: 0.7025 (mtt180) cc_final: 0.6353 (mtm110) REVERT: A 687 ARG cc_start: 0.7415 (mtt180) cc_final: 0.6813 (mtm-85) REVERT: A 709 GLU cc_start: 0.7471 (tt0) cc_final: 0.6227 (mt-10) REVERT: B 161 PHE cc_start: 0.7070 (m-80) cc_final: 0.6710 (m-80) REVERT: B 193 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7948 (mtp85) REVERT: B 221 LYS cc_start: 0.7300 (mttm) cc_final: 0.6927 (mmtp) REVERT: B 289 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7525 (mp0) REVERT: B 309 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 392 ARG cc_start: 0.6596 (ttt90) cc_final: 0.6235 (ttp-170) REVERT: B 595 ASP cc_start: 0.5869 (m-30) cc_final: 0.5187 (t0) REVERT: B 613 GLN cc_start: 0.6722 (mm-40) cc_final: 0.5458 (mp10) REVERT: B 647 GLU cc_start: 0.7226 (tt0) cc_final: 0.6963 (pt0) REVERT: B 679 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6407 (mtm110) REVERT: B 687 ARG cc_start: 0.7390 (mtt180) cc_final: 0.6797 (mtm-85) REVERT: B 709 GLU cc_start: 0.7496 (tt0) cc_final: 0.6251 (mt-10) REVERT: C 161 PHE cc_start: 0.7095 (m-80) cc_final: 0.6734 (m-80) REVERT: C 193 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7961 (mtp85) REVERT: C 221 LYS cc_start: 0.7300 (mttm) cc_final: 0.6931 (mmtp) REVERT: C 289 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7533 (mp0) REVERT: C 309 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7446 (mm-30) REVERT: C 392 ARG cc_start: 0.6573 (ttt90) cc_final: 0.6206 (ttp-170) REVERT: C 595 ASP cc_start: 0.5868 (m-30) cc_final: 0.5189 (t0) REVERT: C 647 GLU cc_start: 0.7223 (tt0) cc_final: 0.6959 (pt0) REVERT: C 679 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6405 (mtm110) REVERT: C 687 ARG cc_start: 0.7398 (mtt180) cc_final: 0.6789 (mtm-85) REVERT: C 709 GLU cc_start: 0.7467 (tt0) cc_final: 0.6223 (mt-10) REVERT: D 161 PHE cc_start: 0.7096 (m-80) cc_final: 0.6736 (m-80) REVERT: D 193 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7951 (mtp85) REVERT: D 221 LYS cc_start: 0.7322 (mttm) cc_final: 0.6952 (mmtp) REVERT: D 289 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7524 (mp0) REVERT: D 309 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 392 ARG cc_start: 0.6582 (ttt90) cc_final: 0.6212 (ttp-170) REVERT: D 595 ASP cc_start: 0.5878 (m-30) cc_final: 0.5195 (t0) REVERT: D 613 GLN cc_start: 0.6714 (mm-40) cc_final: 0.5449 (mp10) REVERT: D 647 GLU cc_start: 0.7221 (tt0) cc_final: 0.6954 (pt0) REVERT: D 679 ARG cc_start: 0.7103 (mtt180) cc_final: 0.6420 (mtm110) REVERT: D 687 ARG cc_start: 0.7420 (mtt180) cc_final: 0.6806 (mtm-85) REVERT: D 709 GLU cc_start: 0.7482 (tt0) cc_final: 0.6231 (mt-10) outliers start: 35 outliers final: 8 residues processed: 251 average time/residue: 1.2676 time to fit residues: 361.0253 Evaluate side-chains 242 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 234 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 158 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 174 optimal weight: 8.9990 chunk 201 optimal weight: 0.2980 chunk 13 optimal weight: 0.0570 chunk 4 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.163176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123987 restraints weight = 22609.522| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.28 r_work: 0.3360 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20220 Z= 0.088 Angle : 0.442 8.672 27404 Z= 0.226 Chirality : 0.037 0.149 3100 Planarity : 0.003 0.040 3348 Dihedral : 7.710 58.724 2852 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.91 % Allowed : 13.22 % Favored : 85.88 % 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: 1.91 (0.17), residues: 2392 helix: 1.99 (0.14), residues: 1480 sheet: 0.27 (0.52), residues: 100 loop : 0.13 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 333 HIS 0.003 0.001 HIS C 165 PHE 0.015 0.001 PHE A 405 TYR 0.011 0.001 TYR B 228 ARG 0.002 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 1108) hydrogen bonds : angle 3.83399 ( 3168) covalent geometry : bond 0.00198 (20220) covalent geometry : angle 0.44153 (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 290 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 271 time to evaluate : 2.289 Fit side-chains REVERT: A 122 MET cc_start: 0.6611 (mtt) cc_final: 0.6403 (mtp) REVERT: A 161 PHE cc_start: 0.7070 (m-80) cc_final: 0.6784 (m-80) REVERT: A 221 LYS cc_start: 0.7309 (mttm) cc_final: 0.6790 (mmtp) REVERT: A 289 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7524 (mp0) REVERT: A 309 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 392 ARG cc_start: 0.6608 (ttt90) cc_final: 0.6340 (tpp80) REVERT: A 404 MET cc_start: 0.7527 (mmm) cc_final: 0.7092 (mmp) REVERT: A 433 MET cc_start: 0.6610 (mmp) cc_final: 0.5697 (ttp) REVERT: A 595 ASP cc_start: 0.5920 (m-30) cc_final: 0.5280 (t0) REVERT: A 613 GLN cc_start: 0.6604 (mm-40) cc_final: 0.5247 (mp10) REVERT: A 647 GLU cc_start: 0.7308 (tt0) cc_final: 0.7035 (pt0) REVERT: A 679 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6447 (mtm110) REVERT: A 687 ARG cc_start: 0.7422 (mtt180) cc_final: 0.6837 (mtm-85) REVERT: A 709 GLU cc_start: 0.7382 (tt0) cc_final: 0.6186 (mt-10) REVERT: B 122 MET cc_start: 0.6672 (mtt) cc_final: 0.6449 (mtp) REVERT: B 161 PHE cc_start: 0.7050 (m-80) cc_final: 0.6763 (m-80) REVERT: B 221 LYS cc_start: 0.7293 (mttm) cc_final: 0.6772 (mmtp) REVERT: B 289 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7519 (mp0) REVERT: B 309 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 383 GLN cc_start: 0.7545 (tp40) cc_final: 0.7340 (tp-100) REVERT: B 392 ARG cc_start: 0.6622 (ttt90) cc_final: 0.6354 (tpp80) REVERT: B 404 MET cc_start: 0.7519 (mmm) cc_final: 0.7084 (mmp) REVERT: B 433 MET cc_start: 0.6631 (mmp) cc_final: 0.5718 (ttp) REVERT: B 595 ASP cc_start: 0.5864 (m-30) cc_final: 0.5227 (t0) REVERT: B 613 GLN cc_start: 0.6616 (mm-40) cc_final: 0.5254 (mp10) REVERT: B 647 GLU cc_start: 0.7302 (tt0) cc_final: 0.7032 (pt0) REVERT: B 679 ARG cc_start: 0.7080 (mtt180) cc_final: 0.6444 (mtm110) REVERT: B 687 ARG cc_start: 0.7406 (mtt180) cc_final: 0.6820 (mtm-85) REVERT: B 709 GLU cc_start: 0.7369 (tt0) cc_final: 0.6178 (mt-10) REVERT: C 122 MET cc_start: 0.6683 (mtt) cc_final: 0.6462 (mtp) REVERT: C 161 PHE cc_start: 0.7098 (m-80) cc_final: 0.6804 (m-80) REVERT: C 221 LYS cc_start: 0.7290 (mttm) cc_final: 0.6772 (mmtp) REVERT: C 289 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7544 (mp0) REVERT: C 309 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7307 (mm-30) REVERT: C 383 GLN cc_start: 0.7527 (tp40) cc_final: 0.7326 (tp-100) REVERT: C 392 ARG cc_start: 0.6589 (ttt90) cc_final: 0.6316 (tpp80) REVERT: C 404 MET cc_start: 0.7491 (mmm) cc_final: 0.7056 (mmp) REVERT: C 433 MET cc_start: 0.6591 (mmp) cc_final: 0.5684 (ttp) REVERT: C 595 ASP cc_start: 0.5819 (m-30) cc_final: 0.5186 (t0) REVERT: C 613 GLN cc_start: 0.6614 (mm-40) cc_final: 0.5300 (mp10) REVERT: C 647 GLU cc_start: 0.7290 (tt0) cc_final: 0.7015 (pt0) REVERT: C 679 ARG cc_start: 0.7072 (mtt180) cc_final: 0.6446 (mtm110) REVERT: C 687 ARG cc_start: 0.7412 (mtt180) cc_final: 0.6819 (mtm-85) REVERT: C 709 GLU cc_start: 0.7392 (tt0) cc_final: 0.6202 (mt-10) REVERT: D 122 MET cc_start: 0.6684 (mtt) cc_final: 0.6461 (mtp) REVERT: D 161 PHE cc_start: 0.7079 (m-80) cc_final: 0.6788 (m-80) REVERT: D 221 LYS cc_start: 0.7297 (mttm) cc_final: 0.6776 (mmtp) REVERT: D 289 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7543 (mp0) REVERT: D 309 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7253 (mm-30) REVERT: D 383 GLN cc_start: 0.7503 (tp40) cc_final: 0.7302 (tp-100) REVERT: D 392 ARG cc_start: 0.6618 (ttt90) cc_final: 0.6345 (tpp80) REVERT: D 404 MET cc_start: 0.7492 (mmm) cc_final: 0.7071 (mmp) REVERT: D 433 MET cc_start: 0.6598 (mmp) cc_final: 0.5689 (ttp) REVERT: D 595 ASP cc_start: 0.5824 (m-30) cc_final: 0.5190 (t0) REVERT: D 613 GLN cc_start: 0.6608 (mm-40) cc_final: 0.5289 (mp10) REVERT: D 647 GLU cc_start: 0.7268 (tt0) cc_final: 0.6995 (pt0) REVERT: D 679 ARG cc_start: 0.7088 (mtt180) cc_final: 0.6450 (mtm110) REVERT: D 687 ARG cc_start: 0.7433 (mtt180) cc_final: 0.6835 (mtm-85) REVERT: D 709 GLU cc_start: 0.7386 (tt0) cc_final: 0.6186 (mt-10) outliers start: 19 outliers final: 9 residues processed: 274 average time/residue: 1.1683 time to fit residues: 366.3359 Evaluate side-chains 258 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 249 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 158 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.157646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117796 restraints weight = 22909.830| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.35 r_work: 0.3285 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20220 Z= 0.194 Angle : 0.554 7.404 27404 Z= 0.276 Chirality : 0.042 0.224 3100 Planarity : 0.004 0.041 3348 Dihedral : 8.536 75.553 2852 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.62 % Allowed : 13.07 % Favored : 85.31 % 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: 1.47 (0.17), residues: 2392 helix: 1.64 (0.13), residues: 1480 sheet: -0.02 (0.53), residues: 100 loop : -0.03 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 333 HIS 0.005 0.001 HIS B 251 PHE 0.018 0.002 PHE D 405 TYR 0.017 0.002 TYR B 228 ARG 0.003 0.000 ARG C 458 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 1108) hydrogen bonds : angle 4.07040 ( 3168) covalent geometry : bond 0.00484 (20220) covalent geometry : angle 0.55427 (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 274 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 2.142 Fit side-chains REVERT: A 161 PHE cc_start: 0.7071 (m-80) cc_final: 0.6734 (m-80) REVERT: A 186 ASN cc_start: 0.6747 (m110) cc_final: 0.6537 (m-40) REVERT: A 221 LYS cc_start: 0.7296 (mttm) cc_final: 0.6898 (mmtp) REVERT: A 228 TYR cc_start: 0.7343 (t80) cc_final: 0.6944 (t80) REVERT: A 289 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7532 (mp0) REVERT: A 309 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 392 ARG cc_start: 0.6610 (ttt90) cc_final: 0.6234 (ttp-170) REVERT: A 595 ASP cc_start: 0.5886 (m-30) cc_final: 0.5200 (t0) REVERT: A 647 GLU cc_start: 0.7120 (tt0) cc_final: 0.6594 (pt0) REVERT: A 679 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6462 (mtm110) REVERT: A 683 HIS cc_start: 0.6374 (t-90) cc_final: 0.6041 (t-90) REVERT: A 687 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6692 (mtm-85) REVERT: A 709 GLU cc_start: 0.7560 (tt0) cc_final: 0.6242 (mt-10) REVERT: B 161 PHE cc_start: 0.7030 (m-80) cc_final: 0.6695 (m-80) REVERT: B 186 ASN cc_start: 0.6764 (m110) cc_final: 0.6562 (m-40) REVERT: B 221 LYS cc_start: 0.7289 (mttm) cc_final: 0.6889 (mmtp) REVERT: B 228 TYR cc_start: 0.7347 (t80) cc_final: 0.6949 (t80) REVERT: B 289 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7542 (mp0) REVERT: B 309 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7407 (mm-30) REVERT: B 392 ARG cc_start: 0.6623 (ttt90) cc_final: 0.6249 (ttp-170) REVERT: B 595 ASP cc_start: 0.5851 (m-30) cc_final: 0.5171 (t0) REVERT: B 641 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6680 (mp) REVERT: B 647 GLU cc_start: 0.7184 (tt0) cc_final: 0.6664 (pt0) REVERT: B 679 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6458 (mtm110) REVERT: B 687 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6699 (mtm-85) REVERT: B 709 GLU cc_start: 0.7555 (tt0) cc_final: 0.6244 (mt-10) REVERT: C 161 PHE cc_start: 0.7059 (m-80) cc_final: 0.6716 (m-80) REVERT: C 221 LYS cc_start: 0.7304 (mttm) cc_final: 0.6906 (mmtp) REVERT: C 228 TYR cc_start: 0.7341 (t80) cc_final: 0.6948 (t80) REVERT: C 289 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7555 (mp0) REVERT: C 309 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 392 ARG cc_start: 0.6600 (ttt90) cc_final: 0.6224 (ttp-170) REVERT: C 595 ASP cc_start: 0.5812 (m-30) cc_final: 0.5141 (t0) REVERT: C 647 GLU cc_start: 0.7171 (tt0) cc_final: 0.6662 (pt0) REVERT: C 679 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6457 (mtm110) REVERT: C 687 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6704 (mtm-85) REVERT: C 709 GLU cc_start: 0.7521 (tt0) cc_final: 0.6209 (mt-10) REVERT: D 161 PHE cc_start: 0.7068 (m-80) cc_final: 0.6731 (m-80) REVERT: D 221 LYS cc_start: 0.7301 (mttm) cc_final: 0.6905 (mmtp) REVERT: D 228 TYR cc_start: 0.7359 (t80) cc_final: 0.6960 (t80) REVERT: D 289 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7537 (mp0) REVERT: D 309 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7394 (mm-30) REVERT: D 392 ARG cc_start: 0.6614 (ttt90) cc_final: 0.6236 (ttp-170) REVERT: D 595 ASP cc_start: 0.5824 (m-30) cc_final: 0.5150 (t0) REVERT: D 647 GLU cc_start: 0.7170 (tt0) cc_final: 0.6658 (pt0) REVERT: D 679 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6461 (mtm110) REVERT: D 687 ARG cc_start: 0.7375 (mtt180) cc_final: 0.6721 (mtm-85) REVERT: D 709 GLU cc_start: 0.7542 (tt0) cc_final: 0.6225 (mt-10) outliers start: 34 outliers final: 21 residues processed: 264 average time/residue: 1.1782 time to fit residues: 356.1485 Evaluate side-chains 253 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 231 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 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 502 VAL Chi-restraints excluded: chain C residue 521 HIS 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 502 VAL Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 621 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118660 restraints weight = 22848.917| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.35 r_work: 0.3296 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20220 Z= 0.152 Angle : 0.503 5.520 27404 Z= 0.255 Chirality : 0.040 0.185 3100 Planarity : 0.004 0.041 3348 Dihedral : 8.464 72.750 2852 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.43 % Allowed : 13.93 % Favored : 84.64 % 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: 1.46 (0.17), residues: 2392 helix: 1.64 (0.13), residues: 1480 sheet: -0.07 (0.53), residues: 100 loop : -0.04 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 333 HIS 0.004 0.001 HIS D 251 PHE 0.019 0.001 PHE D 405 TYR 0.014 0.001 TYR D 228 ARG 0.001 0.000 ARG B 458 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 1108) hydrogen bonds : angle 4.01510 ( 3168) covalent geometry : bond 0.00376 (20220) covalent geometry : angle 0.50310 (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 273 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 243 time to evaluate : 2.163 Fit side-chains REVERT: A 122 MET cc_start: 0.6679 (mtt) cc_final: 0.6448 (mtp) REVERT: A 161 PHE cc_start: 0.7064 (m-80) cc_final: 0.6724 (m-80) REVERT: A 186 ASN cc_start: 0.6803 (m110) cc_final: 0.6569 (m-40) REVERT: A 221 LYS cc_start: 0.7293 (mttm) cc_final: 0.6900 (mmtp) REVERT: A 228 TYR cc_start: 0.7372 (t80) cc_final: 0.6975 (t80) REVERT: A 289 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7528 (mp0) REVERT: A 309 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 392 ARG cc_start: 0.6586 (ttt90) cc_final: 0.6218 (ttp-170) REVERT: A 595 ASP cc_start: 0.5871 (m-30) cc_final: 0.5191 (t0) REVERT: A 609 GLU cc_start: 0.6641 (mt-10) cc_final: 0.5766 (tp30) REVERT: A 641 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6674 (mp) REVERT: A 647 GLU cc_start: 0.7097 (tt0) cc_final: 0.6557 (pt0) REVERT: A 679 ARG cc_start: 0.7133 (mtt180) cc_final: 0.6458 (mtm110) REVERT: A 687 ARG cc_start: 0.7343 (mtt180) cc_final: 0.6696 (mtm-85) REVERT: A 709 GLU cc_start: 0.7525 (tt0) cc_final: 0.6220 (mt-10) REVERT: B 122 MET cc_start: 0.6703 (mtt) cc_final: 0.6463 (mtp) REVERT: B 161 PHE cc_start: 0.7021 (m-80) cc_final: 0.6685 (m-80) REVERT: B 221 LYS cc_start: 0.7277 (mttm) cc_final: 0.6883 (mmtp) REVERT: B 228 TYR cc_start: 0.7380 (t80) cc_final: 0.6985 (t80) REVERT: B 289 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7539 (mp0) REVERT: B 309 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 392 ARG cc_start: 0.6597 (ttt90) cc_final: 0.6231 (ttp-170) REVERT: B 595 ASP cc_start: 0.5854 (m-30) cc_final: 0.5171 (t0) REVERT: B 609 GLU cc_start: 0.6638 (mt-10) cc_final: 0.5760 (tp30) REVERT: B 647 GLU cc_start: 0.7082 (tt0) cc_final: 0.6583 (pt0) REVERT: B 679 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6459 (mtm110) REVERT: B 687 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6688 (mtm-85) REVERT: B 709 GLU cc_start: 0.7525 (tt0) cc_final: 0.6227 (mt-10) REVERT: C 161 PHE cc_start: 0.7081 (m-80) cc_final: 0.6731 (m-80) REVERT: C 193 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7942 (mtp85) REVERT: C 221 LYS cc_start: 0.7296 (mttm) cc_final: 0.6904 (mmtp) REVERT: C 228 TYR cc_start: 0.7361 (t80) cc_final: 0.6972 (t80) REVERT: C 289 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7553 (mp0) REVERT: C 309 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7443 (mm-30) REVERT: C 392 ARG cc_start: 0.6581 (ttt90) cc_final: 0.6211 (ttp-170) REVERT: C 595 ASP cc_start: 0.5798 (m-30) cc_final: 0.5125 (t0) REVERT: C 609 GLU cc_start: 0.6641 (mt-10) cc_final: 0.5777 (tp30) REVERT: C 647 GLU cc_start: 0.7096 (tt0) cc_final: 0.6564 (pt0) REVERT: C 679 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6453 (mtm110) REVERT: C 687 ARG cc_start: 0.7345 (mtt180) cc_final: 0.6694 (mtm-85) REVERT: C 709 GLU cc_start: 0.7498 (tt0) cc_final: 0.6200 (mt-10) REVERT: D 122 MET cc_start: 0.6690 (mtt) cc_final: 0.6456 (mtp) REVERT: D 161 PHE cc_start: 0.7085 (m-80) cc_final: 0.6741 (m-80) REVERT: D 193 ARG cc_start: 0.8156 (mtp180) cc_final: 0.7932 (mtp85) REVERT: D 221 LYS cc_start: 0.7284 (mttm) cc_final: 0.6893 (mmtp) REVERT: D 228 TYR cc_start: 0.7381 (t80) cc_final: 0.6987 (t80) REVERT: D 289 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7530 (mp0) REVERT: D 309 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7396 (mm-30) REVERT: D 392 ARG cc_start: 0.6593 (ttt90) cc_final: 0.6223 (ttp-170) REVERT: D 595 ASP cc_start: 0.5820 (m-30) cc_final: 0.5144 (t0) REVERT: D 609 GLU cc_start: 0.6648 (mt-10) cc_final: 0.5773 (tp30) REVERT: D 647 GLU cc_start: 0.7147 (tt0) cc_final: 0.6614 (pt0) REVERT: D 679 ARG cc_start: 0.7140 (mtt180) cc_final: 0.6467 (mtm110) REVERT: D 687 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6713 (mtm-85) REVERT: D 709 GLU cc_start: 0.7507 (tt0) cc_final: 0.6205 (mt-10) outliers start: 30 outliers final: 17 residues processed: 263 average time/residue: 1.2615 time to fit residues: 379.3522 Evaluate side-chains 251 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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 502 VAL 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 502 VAL 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 502 VAL 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 461 LEU Chi-restraints excluded: chain D residue 502 VAL 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: 3.9990 chunk 212 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 145 optimal weight: 0.0030 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 0.1980 chunk 200 optimal weight: 3.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.159470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119602 restraints weight = 22717.082| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.35 r_work: 0.3310 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20220 Z= 0.123 Angle : 0.504 9.146 27404 Z= 0.251 Chirality : 0.039 0.173 3100 Planarity : 0.003 0.041 3348 Dihedral : 8.360 70.926 2852 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.34 % Allowed : 13.84 % Favored : 84.83 % 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: 1.59 (0.17), residues: 2392 helix: 1.75 (0.13), residues: 1480 sheet: -0.09 (0.52), residues: 100 loop : -0.01 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 333 HIS 0.004 0.001 HIS A 251 PHE 0.019 0.001 PHE C 405 TYR 0.013 0.001 TYR C 228 ARG 0.002 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 1108) hydrogen bonds : angle 3.97160 ( 3168) covalent geometry : bond 0.00299 (20220) covalent geometry : angle 0.50384 (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 271 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 2.323 Fit side-chains REVERT: A 122 MET cc_start: 0.6674 (mtt) cc_final: 0.6474 (mtp) REVERT: A 161 PHE cc_start: 0.7059 (m-80) cc_final: 0.6745 (m-80) REVERT: A 193 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7929 (mtp85) REVERT: A 221 LYS cc_start: 0.7272 (mttm) cc_final: 0.6874 (mmtp) REVERT: A 289 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7555 (mp0) REVERT: A 309 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 392 ARG cc_start: 0.6603 (ttt90) cc_final: 0.6246 (ttp-170) REVERT: A 595 ASP cc_start: 0.5874 (m-30) cc_final: 0.5199 (t0) REVERT: A 641 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6650 (mp) REVERT: A 647 GLU cc_start: 0.7097 (tt0) cc_final: 0.6557 (pt0) REVERT: A 679 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6461 (mtm110) REVERT: A 687 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6698 (mtm-85) REVERT: A 709 GLU cc_start: 0.7478 (tt0) cc_final: 0.6183 (mt-10) REVERT: B 122 MET cc_start: 0.6706 (mtt) cc_final: 0.6497 (mtp) REVERT: B 161 PHE cc_start: 0.7027 (m-80) cc_final: 0.6696 (m-80) REVERT: B 193 ARG cc_start: 0.8154 (mtp180) cc_final: 0.7929 (mtp85) REVERT: B 221 LYS cc_start: 0.7248 (mttm) cc_final: 0.6850 (mmtp) REVERT: B 289 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7546 (mp0) REVERT: B 309 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7444 (mm-30) REVERT: B 392 ARG cc_start: 0.6612 (ttt90) cc_final: 0.6259 (ttp-170) REVERT: B 595 ASP cc_start: 0.5835 (m-30) cc_final: 0.5164 (t0) REVERT: B 641 LEU cc_start: 0.7088 (mp) cc_final: 0.6676 (mp) REVERT: B 647 GLU cc_start: 0.7094 (tt0) cc_final: 0.6584 (pt0) REVERT: B 679 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6465 (mtm110) REVERT: B 687 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6698 (mtm-85) REVERT: B 709 GLU cc_start: 0.7480 (tt0) cc_final: 0.6188 (mt-10) REVERT: C 161 PHE cc_start: 0.7084 (m-80) cc_final: 0.6748 (m-80) REVERT: C 193 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7940 (mtp85) REVERT: C 221 LYS cc_start: 0.7264 (mttm) cc_final: 0.6867 (mmtp) REVERT: C 289 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7567 (mp0) REVERT: C 309 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7443 (mm-30) REVERT: C 392 ARG cc_start: 0.6601 (ttt90) cc_final: 0.6246 (ttp-170) REVERT: C 595 ASP cc_start: 0.5793 (m-30) cc_final: 0.5128 (t0) REVERT: C 609 GLU cc_start: 0.6704 (mt-10) cc_final: 0.5802 (tp30) REVERT: C 647 GLU cc_start: 0.7111 (tt0) cc_final: 0.6568 (pt0) REVERT: C 679 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6460 (mtm110) REVERT: C 687 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6687 (mtm-85) REVERT: C 709 GLU cc_start: 0.7471 (tt0) cc_final: 0.6183 (mt-10) REVERT: D 122 MET cc_start: 0.6695 (mtt) cc_final: 0.6489 (mtp) REVERT: D 161 PHE cc_start: 0.7090 (m-80) cc_final: 0.6754 (m-80) REVERT: D 193 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7928 (mtp85) REVERT: D 221 LYS cc_start: 0.7260 (mttm) cc_final: 0.6863 (mmtp) REVERT: D 289 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7554 (mp0) REVERT: D 309 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7442 (mm-30) REVERT: D 392 ARG cc_start: 0.6621 (ttt90) cc_final: 0.6262 (ttp-170) REVERT: D 595 ASP cc_start: 0.5787 (m-30) cc_final: 0.5124 (t0) REVERT: D 609 GLU cc_start: 0.6700 (mt-10) cc_final: 0.5798 (tp30) REVERT: D 647 GLU cc_start: 0.7100 (tt0) cc_final: 0.6562 (pt0) REVERT: D 679 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6461 (mtm110) REVERT: D 687 ARG cc_start: 0.7355 (mtt180) cc_final: 0.6706 (mtm-85) REVERT: D 709 GLU cc_start: 0.7489 (tt0) cc_final: 0.6193 (mt-10) outliers start: 28 outliers final: 20 residues processed: 263 average time/residue: 1.3031 time to fit residues: 389.3684 Evaluate side-chains 255 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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 502 VAL Chi-restraints excluded: chain A residue 521 HIS 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 502 VAL Chi-restraints excluded: chain B residue 521 HIS 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 502 VAL Chi-restraints excluded: chain C residue 521 HIS 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 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 136 optimal weight: 0.7980 chunk 228 optimal weight: 0.1980 chunk 143 optimal weight: 0.6980 chunk 196 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.161183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121728 restraints weight = 22911.399| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.29 r_work: 0.3341 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20220 Z= 0.101 Angle : 0.453 5.574 27404 Z= 0.232 Chirality : 0.038 0.154 3100 Planarity : 0.003 0.041 3348 Dihedral : 8.142 66.025 2852 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.15 % Allowed : 13.84 % Favored : 85.02 % 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: 1.88 (0.14), residues: 1484 sheet: -0.02 (0.51), residues: 100 loop : -0.02 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 333 HIS 0.003 0.001 HIS A 251 PHE 0.019 0.001 PHE C 405 TYR 0.012 0.001 TYR D 228 ARG 0.002 0.000 ARG B 339 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 1108) hydrogen bonds : angle 3.88447 ( 3168) covalent geometry : bond 0.00237 (20220) covalent geometry : angle 0.45310 (27404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14537.46 seconds wall clock time: 248 minutes 11.96 seconds (14891.96 seconds total)