Starting phenix.real_space_refine on Thu Mar 5 04:35:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zji_14749/03_2026/7zji_14749.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zji_14749/03_2026/7zji_14749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zji_14749/03_2026/7zji_14749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zji_14749/03_2026/7zji_14749.map" model { file = "/net/cci-nas-00/data/ceres_data/7zji_14749/03_2026/7zji_14749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zji_14749/03_2026/7zji_14749.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12641 2.51 5 N 3203 2.21 5 O 3275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19231 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4809 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4804 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4809 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4809 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.33, per 1000 atoms: 0.23 Number of scatterers: 19231 At special positions: 0 Unit cell: (126.114, 156.584, 153.198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3275 8.00 N 3203 7.00 C 12641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 677.9 milliseconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4486 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 56.6% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 135 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.661A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.846A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.574A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.238A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.641A pdb=" N MET B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 470 through 490 removed outlier: 3.793A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 494 through 495 No H-bonds generated for 'chain 'B' and resid 494 through 495' Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.889A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 522 through 543 removed outlier: 3.999A pdb=" N SER B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 559 Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 627 through 650 removed outlier: 4.073A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 674 removed outlier: 4.461A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 119 through 125 removed outlier: 3.794A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.967A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.525A pdb=" N SER A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.022A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.640A pdb=" N HIS A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.688A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 516 removed outlier: 4.181A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.928A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 3.542A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 595 through 605 removed outlier: 4.258A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 628 through 647 removed outlier: 3.735A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 674 removed outlier: 4.333A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.614A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.734A pdb=" N LYS C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.831A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.779A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.550A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.121A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 375 through 387 Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 470 through 491 removed outlier: 3.745A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 516 removed outlier: 3.837A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 534 removed outlier: 3.732A pdb=" N SER C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 541 removed outlier: 4.056A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 5.001A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.922A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 650 removed outlier: 4.662A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 674 removed outlier: 4.091A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 674 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.547A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.584A pdb=" N LYS D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.890A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.542A pdb=" N GLU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.591A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.510A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.170A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.530A pdb=" N MET D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.733A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.518A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 516 removed outlier: 4.488A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 528 removed outlier: 3.550A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.705A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 544 " --> pdb=" O PHE D 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 539 through 544' Processing helix chain 'D' and resid 544 through 557 removed outlier: 3.949A pdb=" N GLY D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 551 " --> pdb=" O PHE D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 removed outlier: 3.564A pdb=" N SER D 597 " --> pdb=" O ILE D 593 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU D 598 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 649 removed outlier: 4.151A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 644 " --> pdb=" O MET D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 674 removed outlier: 4.066A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 715 removed outlier: 3.682A pdb=" N TRP D 715 " --> pdb=" O TRP D 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.584A pdb=" N CYS B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 687 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.564A pdb=" N CYS D 704 " --> pdb=" O ARG D 687 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 687 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5944 1.34 - 1.46: 4559 1.46 - 1.58: 9044 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 19719 Sorted by residual: bond pdb=" N ASP A 108 " pdb=" CA ASP A 108 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N PHE A 601 " pdb=" CA PHE A 601 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.33e-02 5.65e+03 7.25e+00 bond pdb=" N HIS D 651 " pdb=" CA HIS D 651 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" N THR A 604 " pdb=" CA THR A 604 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N VAL D 652 " pdb=" CA VAL D 652 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.14e-02 7.69e+03 5.91e+00 ... (remaining 19714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 26130 1.88 - 3.75: 514 3.75 - 5.63: 91 5.63 - 7.50: 20 7.50 - 9.38: 5 Bond angle restraints: 26760 Sorted by residual: angle pdb=" N ASP D 654 " pdb=" CA ASP D 654 " pdb=" C ASP D 654 " ideal model delta sigma weight residual 114.16 104.78 9.38 1.48e+00 4.57e-01 4.01e+01 angle pdb=" N LEU D 641 " pdb=" CA LEU D 641 " pdb=" C LEU D 641 " ideal model delta sigma weight residual 113.18 105.24 7.94 1.33e+00 5.65e-01 3.57e+01 angle pdb=" N VAL C 621 " pdb=" CA VAL C 621 " pdb=" C VAL C 621 " ideal model delta sigma weight residual 113.43 107.90 5.53 1.09e+00 8.42e-01 2.57e+01 angle pdb=" CA LEU D 641 " pdb=" C LEU D 641 " pdb=" N ILE D 642 " ideal model delta sigma weight residual 118.22 113.58 4.64 1.03e+00 9.43e-01 2.03e+01 angle pdb=" N TYR A 525 " pdb=" CA TYR A 525 " pdb=" C TYR A 525 " ideal model delta sigma weight residual 114.62 109.58 5.04 1.14e+00 7.69e-01 1.95e+01 ... (remaining 26755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10358 17.92 - 35.83: 946 35.83 - 53.74: 183 53.74 - 71.66: 21 71.66 - 89.57: 17 Dihedral angle restraints: 11525 sinusoidal: 4580 harmonic: 6945 Sorted by residual: dihedral pdb=" CA TRP A 464 " pdb=" C TRP A 464 " pdb=" N ILE A 465 " pdb=" CA ILE A 465 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU D 345 " pdb=" C LEU D 345 " pdb=" N SER D 346 " pdb=" CA SER D 346 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2321 0.045 - 0.090: 608 0.090 - 0.135: 89 0.135 - 0.179: 10 0.179 - 0.224: 3 Chirality restraints: 3031 Sorted by residual: chirality pdb=" CB ILE C 158 " pdb=" CA ILE C 158 " pdb=" CG1 ILE C 158 " pdb=" CG2 ILE C 158 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA MET D 137 " pdb=" N MET D 137 " pdb=" C MET D 137 " pdb=" CB MET D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR A 604 " pdb=" CA THR A 604 " pdb=" OG1 THR A 604 " pdb=" CG2 THR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 3028 not shown) Planarity restraints: 3286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 150 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO C 151 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 601 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C PHE A 601 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 601 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 602 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 601 " 0.017 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE D 601 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 601 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 601 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 601 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 601 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 601 " 0.003 2.00e-02 2.50e+03 ... (remaining 3283 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1408 2.74 - 3.28: 19917 3.28 - 3.82: 30145 3.82 - 4.36: 34379 4.36 - 4.90: 58561 Nonbonded interactions: 144410 Sorted by model distance: nonbonded pdb=" O PHE B 601 " pdb=" OG1 THR B 604 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR A 525 " pdb=" NH1 ARG D 535 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR A 412 " pdb=" O SER D 592 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR C 271 " pdb=" OE2 GLU C 288 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR B 271 " pdb=" OE2 GLU B 288 " model vdw 2.239 3.040 ... (remaining 144405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 75 through 559 or resid 589 through 716)) selection = (chain 'C' and (resid 75 through 559 or resid 589 through 716)) selection = (chain 'D' and (resid 75 through 559 or resid 589 through 716)) } 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.560 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19719 Z= 0.137 Angle : 0.658 9.376 26760 Z= 0.362 Chirality : 0.040 0.224 3031 Planarity : 0.004 0.088 3286 Dihedral : 14.202 89.574 7039 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.28 % Favored : 91.46 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2343 helix: 1.18 (0.16), residues: 1209 sheet: -1.61 (0.62), residues: 61 loop : -2.68 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 539 TYR 0.024 0.001 TYR D 471 PHE 0.035 0.001 PHE D 601 TRP 0.028 0.001 TRP A 464 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00265 (19719) covalent geometry : angle 0.65804 (26760) hydrogen bonds : bond 0.13964 ( 849) hydrogen bonds : angle 5.46212 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 MET cc_start: 0.7766 (mpp) cc_final: 0.7524 (mpp) REVERT: B 645 MET cc_start: 0.8880 (mpp) cc_final: 0.8489 (mpp) REVERT: A 137 MET cc_start: 0.6914 (mmp) cc_final: 0.6472 (tpp) REVERT: A 141 GLN cc_start: 0.7988 (pp30) cc_final: 0.7722 (pp30) REVERT: A 645 MET cc_start: 0.9114 (tmm) cc_final: 0.8763 (tmm) REVERT: C 602 LYS cc_start: 0.9395 (tppt) cc_final: 0.9067 (tppt) REVERT: C 603 PHE cc_start: 0.8123 (m-10) cc_final: 0.7650 (m-80) REVERT: D 81 PHE cc_start: 0.5319 (m-80) cc_final: 0.5105 (m-10) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.1161 time to fit residues: 50.8275 Evaluate side-chains 221 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 HIS ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.177451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125700 restraints weight = 35602.459| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.18 r_work: 0.3392 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 19719 Z= 0.284 Angle : 0.758 7.707 26760 Z= 0.381 Chirality : 0.044 0.174 3031 Planarity : 0.005 0.058 3286 Dihedral : 4.806 30.894 2583 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.86 % Favored : 89.88 % Rotamer: Outliers : 1.50 % Allowed : 10.71 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.17), residues: 2343 helix: 0.78 (0.15), residues: 1226 sheet: -2.47 (0.55), residues: 73 loop : -2.75 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 317 TYR 0.026 0.002 TYR A 544 PHE 0.031 0.002 PHE C 705 TRP 0.026 0.002 TRP B 703 HIS 0.010 0.002 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00685 (19719) covalent geometry : angle 0.75839 (26760) hydrogen bonds : bond 0.05331 ( 849) hydrogen bonds : angle 4.56099 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 681 LYS cc_start: 0.7947 (mttp) cc_final: 0.7546 (pttp) REVERT: A 137 MET cc_start: 0.7732 (mmp) cc_final: 0.7205 (tpp) REVERT: A 141 GLN cc_start: 0.8411 (pp30) cc_final: 0.8012 (pp30) REVERT: A 339 ARG cc_start: 0.6625 (mtp85) cc_final: 0.6294 (mtm180) REVERT: C 528 MET cc_start: 0.8772 (tpt) cc_final: 0.8430 (mtt) REVERT: C 603 PHE cc_start: 0.8410 (m-10) cc_final: 0.7953 (m-80) REVERT: D 81 PHE cc_start: 0.5789 (m-80) cc_final: 0.5351 (m-10) REVERT: D 163 GLN cc_start: 0.5880 (tp-100) cc_final: 0.5644 (tm-30) REVERT: D 468 MET cc_start: 0.8162 (tmm) cc_final: 0.7866 (tmm) REVERT: D 672 GLU cc_start: 0.8594 (tp30) cc_final: 0.8394 (tt0) REVERT: D 676 TRP cc_start: 0.7165 (p-90) cc_final: 0.6757 (p-90) outliers start: 31 outliers final: 24 residues processed: 258 average time/residue: 0.1223 time to fit residues: 50.2663 Evaluate side-chains 237 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 663 GLN Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 170 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.182029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132032 restraints weight = 36004.789| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 4.14 r_work: 0.3482 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19719 Z= 0.112 Angle : 0.588 8.405 26760 Z= 0.290 Chirality : 0.038 0.169 3031 Planarity : 0.003 0.045 3286 Dihedral : 4.291 32.511 2583 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.73 % Favored : 92.02 % Rotamer: Outliers : 1.35 % Allowed : 13.27 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.18), residues: 2343 helix: 1.29 (0.15), residues: 1221 sheet: -2.14 (0.57), residues: 68 loop : -2.75 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 371 TYR 0.022 0.001 TYR B 471 PHE 0.018 0.001 PHE D 395 TRP 0.018 0.001 TRP A 676 HIS 0.005 0.001 HIS D 521 Details of bonding type rmsd covalent geometry : bond 0.00249 (19719) covalent geometry : angle 0.58844 (26760) hydrogen bonds : bond 0.03587 ( 849) hydrogen bonds : angle 3.94353 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9019 (tt) REVERT: B 645 MET cc_start: 0.9281 (mmp) cc_final: 0.8895 (mmt) REVERT: B 681 LYS cc_start: 0.7933 (mttp) cc_final: 0.7541 (pttp) REVERT: A 137 MET cc_start: 0.7499 (mmp) cc_final: 0.6913 (tpp) REVERT: A 141 GLN cc_start: 0.8482 (pp30) cc_final: 0.8118 (pp30) REVERT: A 221 LYS cc_start: 0.8735 (tttp) cc_final: 0.8301 (tptt) REVERT: A 277 MET cc_start: 0.8561 (mtp) cc_final: 0.8357 (mtp) REVERT: A 468 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: A 498 LEU cc_start: 0.7218 (tp) cc_final: 0.6906 (tp) REVERT: C 603 PHE cc_start: 0.8328 (m-10) cc_final: 0.7860 (m-80) REVERT: C 607 MET cc_start: 0.3376 (mmm) cc_final: 0.2950 (mmm) REVERT: D 81 PHE cc_start: 0.5745 (m-80) cc_final: 0.5350 (m-10) REVERT: D 404 MET cc_start: 0.4398 (tpt) cc_final: 0.4080 (tpt) REVERT: D 468 MET cc_start: 0.7990 (tmm) cc_final: 0.7773 (tmm) REVERT: D 517 ARG cc_start: 0.8354 (tpt-90) cc_final: 0.7678 (tpt-90) REVERT: D 676 TRP cc_start: 0.7029 (p-90) cc_final: 0.6744 (p-90) outliers start: 28 outliers final: 14 residues processed: 251 average time/residue: 0.1184 time to fit residues: 47.8843 Evaluate side-chains 239 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 365 LYS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 637 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 144 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.180284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129876 restraints weight = 35598.092| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.74 r_work: 0.3477 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19719 Z= 0.142 Angle : 0.613 8.943 26760 Z= 0.301 Chirality : 0.039 0.179 3031 Planarity : 0.003 0.046 3286 Dihedral : 4.270 32.164 2583 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.05 % Favored : 90.70 % Rotamer: Outliers : 2.17 % Allowed : 15.83 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 2343 helix: 1.28 (0.15), residues: 1226 sheet: -2.08 (0.57), residues: 68 loop : -2.69 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.022 0.001 TYR B 471 PHE 0.031 0.001 PHE D 601 TRP 0.012 0.001 TRP D 333 HIS 0.006 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00336 (19719) covalent geometry : angle 0.61252 (26760) hydrogen bonds : bond 0.03833 ( 849) hydrogen bonds : angle 3.91432 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 GLN cc_start: 0.6347 (tp-100) cc_final: 0.6146 (tp-100) REVERT: B 239 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9077 (tt) REVERT: B 645 MET cc_start: 0.9312 (mmp) cc_final: 0.8905 (mmt) REVERT: B 681 LYS cc_start: 0.7919 (mttp) cc_final: 0.7557 (pttp) REVERT: A 137 MET cc_start: 0.7611 (mmp) cc_final: 0.6988 (tpp) REVERT: A 141 GLN cc_start: 0.8490 (pp30) cc_final: 0.8111 (pp30) REVERT: A 221 LYS cc_start: 0.8740 (tttp) cc_final: 0.8318 (tptt) REVERT: A 239 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9030 (tt) REVERT: A 468 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7348 (tmm) REVERT: A 498 LEU cc_start: 0.7072 (tp) cc_final: 0.6708 (tp) REVERT: A 618 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7175 (t80) REVERT: A 629 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: A 645 MET cc_start: 0.9094 (tmm) cc_final: 0.8807 (tmm) REVERT: C 162 TYR cc_start: 0.3703 (OUTLIER) cc_final: 0.2718 (m-10) REVERT: C 528 MET cc_start: 0.9014 (mmm) cc_final: 0.8475 (mtt) REVERT: C 603 PHE cc_start: 0.8381 (m-10) cc_final: 0.7902 (m-80) REVERT: D 81 PHE cc_start: 0.5744 (m-80) cc_final: 0.5353 (m-10) REVERT: D 404 MET cc_start: 0.5011 (tpt) cc_final: 0.4523 (tpt) REVERT: D 517 ARG cc_start: 0.8343 (tpt-90) cc_final: 0.8011 (tpt-90) REVERT: D 672 GLU cc_start: 0.8482 (tp30) cc_final: 0.8142 (tt0) REVERT: D 676 TRP cc_start: 0.7088 (p-90) cc_final: 0.6851 (p-90) outliers start: 45 outliers final: 24 residues processed: 259 average time/residue: 0.1127 time to fit residues: 48.0510 Evaluate side-chains 247 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 629 TYR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 637 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 6 optimal weight: 0.2980 chunk 129 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.178790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127043 restraints weight = 35678.467| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.34 r_work: 0.3420 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19719 Z= 0.172 Angle : 0.644 12.203 26760 Z= 0.315 Chirality : 0.040 0.183 3031 Planarity : 0.004 0.047 3286 Dihedral : 4.363 32.240 2583 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.96 % Favored : 90.78 % Rotamer: Outliers : 3.04 % Allowed : 17.13 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 2343 helix: 1.17 (0.15), residues: 1238 sheet: -1.90 (0.59), residues: 63 loop : -2.70 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 539 TYR 0.021 0.001 TYR B 471 PHE 0.030 0.001 PHE D 601 TRP 0.013 0.001 TRP B 703 HIS 0.008 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00411 (19719) covalent geometry : angle 0.64431 (26760) hydrogen bonds : bond 0.04139 ( 849) hydrogen bonds : angle 3.95998 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 229 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9072 (tt) REVERT: B 384 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8778 (tm-30) REVERT: B 645 MET cc_start: 0.9367 (mmp) cc_final: 0.8949 (mmt) REVERT: B 681 LYS cc_start: 0.7931 (mttp) cc_final: 0.7568 (pttp) REVERT: A 137 MET cc_start: 0.7788 (mmp) cc_final: 0.7213 (tpp) REVERT: A 141 GLN cc_start: 0.8512 (pp30) cc_final: 0.8108 (pp30) REVERT: A 162 TYR cc_start: 0.3281 (OUTLIER) cc_final: 0.3021 (m-10) REVERT: A 221 LYS cc_start: 0.8760 (tttp) cc_final: 0.8308 (tptt) REVERT: A 239 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9074 (tt) REVERT: A 339 ARG cc_start: 0.6650 (mtp85) cc_final: 0.6262 (mtm180) REVERT: A 468 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7274 (tmm) REVERT: A 498 LEU cc_start: 0.7257 (tp) cc_final: 0.6937 (tp) REVERT: A 618 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7182 (t80) REVERT: C 162 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.2550 (m-10) REVERT: C 286 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8458 (mt0) REVERT: C 529 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8724 (mm) REVERT: C 603 PHE cc_start: 0.8380 (m-10) cc_final: 0.7903 (m-80) REVERT: D 81 PHE cc_start: 0.5803 (m-80) cc_final: 0.5320 (m-80) REVERT: D 404 MET cc_start: 0.5206 (tpt) cc_final: 0.4672 (tpt) REVERT: D 517 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.7700 (tpt-90) REVERT: D 672 GLU cc_start: 0.8527 (tp30) cc_final: 0.8194 (tt0) REVERT: D 676 TRP cc_start: 0.7147 (p-90) cc_final: 0.6818 (p-90) outliers start: 63 outliers final: 41 residues processed: 270 average time/residue: 0.1121 time to fit residues: 49.6424 Evaluate side-chains 266 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 351 TRP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 663 GLN Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 223 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 215 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 189 optimal weight: 10.0000 chunk 124 optimal weight: 0.0070 chunk 161 optimal weight: 0.0050 chunk 79 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN A 156 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.182556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132835 restraints weight = 35525.505| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.99 r_work: 0.3494 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19719 Z= 0.101 Angle : 0.601 13.661 26760 Z= 0.288 Chirality : 0.038 0.184 3031 Planarity : 0.003 0.059 3286 Dihedral : 4.036 31.325 2583 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.43 % Favored : 92.36 % Rotamer: Outliers : 2.27 % Allowed : 18.15 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.18), residues: 2343 helix: 1.49 (0.15), residues: 1231 sheet: -1.79 (0.58), residues: 65 loop : -2.67 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 539 TYR 0.022 0.001 TYR B 471 PHE 0.032 0.001 PHE D 601 TRP 0.012 0.001 TRP C 351 HIS 0.004 0.001 HIS D 521 Details of bonding type rmsd covalent geometry : bond 0.00211 (19719) covalent geometry : angle 0.60132 (26760) hydrogen bonds : bond 0.03120 ( 849) hydrogen bonds : angle 3.67707 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8983 (tt) REVERT: B 384 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8773 (tm-30) REVERT: B 681 LYS cc_start: 0.7964 (mttp) cc_final: 0.7623 (pttp) REVERT: A 137 MET cc_start: 0.7664 (mmp) cc_final: 0.7064 (tpp) REVERT: A 141 GLN cc_start: 0.8513 (pp30) cc_final: 0.8159 (pp30) REVERT: A 221 LYS cc_start: 0.8690 (tttp) cc_final: 0.8288 (tptt) REVERT: A 239 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9033 (tt) REVERT: A 277 MET cc_start: 0.8565 (mtp) cc_final: 0.8325 (mtp) REVERT: A 291 SER cc_start: 0.8692 (t) cc_final: 0.8180 (m) REVERT: A 468 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7278 (tpp) REVERT: A 498 LEU cc_start: 0.7156 (tp) cc_final: 0.6893 (tp) REVERT: A 645 MET cc_start: 0.9078 (tmm) cc_final: 0.8805 (tmm) REVERT: C 162 TYR cc_start: 0.3639 (OUTLIER) cc_final: 0.2489 (m-10) REVERT: C 286 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8393 (mt0) REVERT: C 524 ILE cc_start: 0.7787 (mp) cc_final: 0.7181 (mm) REVERT: C 528 MET cc_start: 0.8997 (mmm) cc_final: 0.8538 (mtt) REVERT: C 603 PHE cc_start: 0.8320 (m-10) cc_final: 0.7853 (m-80) REVERT: C 607 MET cc_start: 0.3406 (mmm) cc_final: 0.2739 (mmm) REVERT: D 81 PHE cc_start: 0.5720 (m-80) cc_final: 0.5285 (m-80) REVERT: D 404 MET cc_start: 0.5074 (tpt) cc_final: 0.4750 (tpt) REVERT: D 517 ARG cc_start: 0.8336 (tpt-90) cc_final: 0.7655 (tpt-90) outliers start: 47 outliers final: 32 residues processed: 262 average time/residue: 0.1163 time to fit residues: 50.1769 Evaluate side-chains 249 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 130 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 41 optimal weight: 0.0030 chunk 209 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.182131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.131219 restraints weight = 35850.035| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 4.02 r_work: 0.3490 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19719 Z= 0.110 Angle : 0.626 14.810 26760 Z= 0.298 Chirality : 0.038 0.186 3031 Planarity : 0.003 0.050 3286 Dihedral : 4.031 30.610 2583 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.11 % Favored : 91.72 % Rotamer: Outliers : 2.51 % Allowed : 18.58 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.18), residues: 2343 helix: 1.45 (0.15), residues: 1238 sheet: -1.67 (0.60), residues: 65 loop : -2.69 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 539 TYR 0.021 0.001 TYR B 471 PHE 0.032 0.001 PHE D 601 TRP 0.039 0.001 TRP D 676 HIS 0.004 0.001 HIS D 521 Details of bonding type rmsd covalent geometry : bond 0.00247 (19719) covalent geometry : angle 0.62600 (26760) hydrogen bonds : bond 0.03271 ( 849) hydrogen bonds : angle 3.71661 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 645 MET cc_start: 0.9143 (mmm) cc_final: 0.8840 (mmt) REVERT: B 681 LYS cc_start: 0.7921 (mttp) cc_final: 0.7602 (pttp) REVERT: A 137 MET cc_start: 0.7677 (mmp) cc_final: 0.7094 (tpp) REVERT: A 141 GLN cc_start: 0.8485 (pp30) cc_final: 0.8131 (pp30) REVERT: A 162 TYR cc_start: 0.3382 (OUTLIER) cc_final: 0.2999 (m-10) REVERT: A 221 LYS cc_start: 0.8684 (tttp) cc_final: 0.8307 (tptt) REVERT: A 239 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9039 (tt) REVERT: A 277 MET cc_start: 0.8580 (mtp) cc_final: 0.8315 (mtp) REVERT: A 291 SER cc_start: 0.8714 (t) cc_final: 0.8204 (m) REVERT: A 468 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7250 (tpp) REVERT: A 498 LEU cc_start: 0.7281 (tp) cc_final: 0.6838 (tp) REVERT: A 539 ARG cc_start: 0.8173 (tpt90) cc_final: 0.7930 (tpt90) REVERT: A 645 MET cc_start: 0.9109 (tmm) cc_final: 0.8838 (tmm) REVERT: C 162 TYR cc_start: 0.3718 (OUTLIER) cc_final: 0.2677 (m-10) REVERT: C 286 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8384 (mt0) REVERT: C 517 ARG cc_start: 0.7091 (tpp-160) cc_final: 0.6785 (tpp-160) REVERT: C 524 ILE cc_start: 0.7765 (mp) cc_final: 0.7144 (mm) REVERT: C 528 MET cc_start: 0.8991 (mmm) cc_final: 0.8516 (mtt) REVERT: C 529 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8731 (mm) REVERT: C 603 PHE cc_start: 0.8237 (m-10) cc_final: 0.7763 (m-80) REVERT: C 607 MET cc_start: 0.3386 (mmm) cc_final: 0.2800 (mmm) REVERT: D 81 PHE cc_start: 0.5755 (m-80) cc_final: 0.5316 (m-80) REVERT: D 404 MET cc_start: 0.5274 (tpt) cc_final: 0.4884 (tpt) REVERT: D 517 ARG cc_start: 0.8335 (tpt-90) cc_final: 0.7845 (tpt-90) outliers start: 52 outliers final: 38 residues processed: 256 average time/residue: 0.1158 time to fit residues: 48.2192 Evaluate side-chains 262 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 178 optimal weight: 40.0000 chunk 196 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.176860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125296 restraints weight = 35652.725| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.64 r_work: 0.3425 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 19719 Z= 0.230 Angle : 0.720 12.952 26760 Z= 0.354 Chirality : 0.042 0.251 3031 Planarity : 0.004 0.047 3286 Dihedral : 4.548 32.003 2583 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.69 % Favored : 90.14 % Rotamer: Outliers : 2.99 % Allowed : 19.02 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 2343 helix: 1.07 (0.15), residues: 1225 sheet: -1.66 (0.59), residues: 63 loop : -2.71 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 539 TYR 0.019 0.002 TYR B 471 PHE 0.032 0.002 PHE D 601 TRP 0.053 0.002 TRP D 676 HIS 0.009 0.002 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00556 (19719) covalent geometry : angle 0.72046 (26760) hydrogen bonds : bond 0.04767 ( 849) hydrogen bonds : angle 4.15291 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 221 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 384 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8716 (tm-30) REVERT: B 645 MET cc_start: 0.9167 (mmm) cc_final: 0.8871 (mmt) REVERT: B 681 LYS cc_start: 0.7960 (mttp) cc_final: 0.7643 (pttp) REVERT: A 137 MET cc_start: 0.7918 (mmp) cc_final: 0.7595 (tpp) REVERT: A 141 GLN cc_start: 0.8469 (pp30) cc_final: 0.8007 (pp30) REVERT: A 162 TYR cc_start: 0.3519 (OUTLIER) cc_final: 0.3221 (m-10) REVERT: A 221 LYS cc_start: 0.8789 (tttp) cc_final: 0.8347 (tptt) REVERT: A 239 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9080 (tt) REVERT: A 339 ARG cc_start: 0.6649 (mtp85) cc_final: 0.6317 (mtm180) REVERT: A 468 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7225 (tpp) REVERT: A 498 LEU cc_start: 0.7400 (tp) cc_final: 0.7101 (tp) REVERT: A 645 MET cc_start: 0.9121 (tmm) cc_final: 0.8782 (tmm) REVERT: C 162 TYR cc_start: 0.3850 (OUTLIER) cc_final: 0.2596 (m-10) REVERT: C 286 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8428 (mt0) REVERT: C 517 ARG cc_start: 0.7155 (tpp-160) cc_final: 0.6750 (tpp-160) REVERT: C 524 ILE cc_start: 0.7792 (mp) cc_final: 0.7588 (mm) REVERT: C 529 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8713 (mm) REVERT: C 603 PHE cc_start: 0.8306 (m-10) cc_final: 0.7823 (m-80) REVERT: C 607 MET cc_start: 0.3525 (mmm) cc_final: 0.2853 (mmm) REVERT: D 81 PHE cc_start: 0.5743 (m-80) cc_final: 0.5267 (m-80) REVERT: D 270 MET cc_start: 0.8806 (mmm) cc_final: 0.8494 (tpt) REVERT: D 404 MET cc_start: 0.5502 (tpt) cc_final: 0.4784 (tpt) REVERT: D 517 ARG cc_start: 0.8399 (tpt-90) cc_final: 0.7780 (ttt-90) REVERT: D 672 GLU cc_start: 0.8593 (tp30) cc_final: 0.8186 (tt0) outliers start: 62 outliers final: 44 residues processed: 263 average time/residue: 0.1122 time to fit residues: 48.3276 Evaluate side-chains 262 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 162 TYR Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 351 TRP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.180806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131078 restraints weight = 35583.319| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.91 r_work: 0.3476 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19719 Z= 0.115 Angle : 0.646 13.698 26760 Z= 0.308 Chirality : 0.039 0.196 3031 Planarity : 0.003 0.046 3286 Dihedral : 4.199 31.604 2583 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.94 % Favored : 91.89 % Rotamer: Outliers : 2.36 % Allowed : 20.32 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2343 helix: 1.28 (0.15), residues: 1233 sheet: -1.50 (0.60), residues: 63 loop : -2.72 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 535 TYR 0.021 0.001 TYR B 412 PHE 0.033 0.001 PHE D 601 TRP 0.026 0.001 TRP D 676 HIS 0.004 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00262 (19719) covalent geometry : angle 0.64642 (26760) hydrogen bonds : bond 0.03474 ( 849) hydrogen bonds : angle 3.83162 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8585 (mtt) cc_final: 0.8331 (mtm) REVERT: B 384 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8725 (tm-30) REVERT: B 645 MET cc_start: 0.9128 (mmm) cc_final: 0.8829 (mmt) REVERT: B 681 LYS cc_start: 0.7970 (mttp) cc_final: 0.7621 (pttp) REVERT: A 137 MET cc_start: 0.7836 (mmp) cc_final: 0.7563 (tpp) REVERT: A 141 GLN cc_start: 0.8505 (pp30) cc_final: 0.8044 (pp30) REVERT: A 221 LYS cc_start: 0.8694 (tttp) cc_final: 0.8344 (tptt) REVERT: A 239 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9050 (tt) REVERT: A 245 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8508 (tt) REVERT: A 291 SER cc_start: 0.8694 (t) cc_final: 0.8113 (m) REVERT: A 339 ARG cc_start: 0.6576 (mtp85) cc_final: 0.6244 (mtm180) REVERT: A 468 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7148 (tpp) REVERT: A 498 LEU cc_start: 0.7400 (tp) cc_final: 0.7131 (tp) REVERT: A 542 LEU cc_start: 0.8643 (tt) cc_final: 0.8204 (mt) REVERT: A 645 MET cc_start: 0.9144 (tmm) cc_final: 0.8805 (tmm) REVERT: C 162 TYR cc_start: 0.3795 (OUTLIER) cc_final: 0.2793 (m-10) REVERT: C 286 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8389 (mt0) REVERT: C 524 ILE cc_start: 0.7783 (mp) cc_final: 0.7158 (mm) REVERT: C 528 MET cc_start: 0.8980 (mmm) cc_final: 0.8513 (mtt) REVERT: C 529 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (mm) REVERT: C 603 PHE cc_start: 0.8239 (m-10) cc_final: 0.7767 (m-80) REVERT: C 607 MET cc_start: 0.3472 (mmm) cc_final: 0.2916 (mmm) REVERT: D 81 PHE cc_start: 0.5689 (m-80) cc_final: 0.5246 (m-80) REVERT: D 404 MET cc_start: 0.5302 (tpt) cc_final: 0.4860 (tpt) REVERT: D 512 LEU cc_start: 0.7162 (tp) cc_final: 0.6766 (tp) REVERT: D 517 ARG cc_start: 0.8356 (tpt-90) cc_final: 0.7828 (ttt-90) outliers start: 49 outliers final: 39 residues processed: 253 average time/residue: 0.1183 time to fit residues: 48.9081 Evaluate side-chains 263 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 351 TRP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 0.0060 chunk 132 optimal weight: 0.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.180922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.129837 restraints weight = 35717.106| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.97 r_work: 0.3480 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19719 Z= 0.116 Angle : 0.643 12.908 26760 Z= 0.307 Chirality : 0.038 0.189 3031 Planarity : 0.003 0.046 3286 Dihedral : 4.056 31.292 2583 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.45 % Favored : 91.38 % Rotamer: Outliers : 2.12 % Allowed : 21.04 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.18), residues: 2343 helix: 1.35 (0.15), residues: 1235 sheet: -1.48 (0.60), residues: 65 loop : -2.71 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 535 TYR 0.018 0.001 TYR B 471 PHE 0.032 0.001 PHE D 601 TRP 0.036 0.001 TRP D 677 HIS 0.004 0.001 HIS B 363 Details of bonding type rmsd covalent geometry : bond 0.00266 (19719) covalent geometry : angle 0.64347 (26760) hydrogen bonds : bond 0.03403 ( 849) hydrogen bonds : angle 3.78583 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8534 (mtt) cc_final: 0.8276 (mtm) REVERT: B 384 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8714 (tm-30) REVERT: B 528 MET cc_start: 0.8152 (mpp) cc_final: 0.7783 (mpp) REVERT: B 607 MET cc_start: 0.4450 (tmm) cc_final: 0.3644 (mmp) REVERT: B 645 MET cc_start: 0.9136 (mmm) cc_final: 0.8831 (mmt) REVERT: B 681 LYS cc_start: 0.7947 (mttp) cc_final: 0.7631 (pttp) REVERT: A 137 MET cc_start: 0.7776 (mmp) cc_final: 0.7503 (tpp) REVERT: A 141 GLN cc_start: 0.8485 (pp30) cc_final: 0.8013 (pp30) REVERT: A 221 LYS cc_start: 0.8637 (tttp) cc_final: 0.8296 (tptt) REVERT: A 239 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9034 (tt) REVERT: A 245 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 291 SER cc_start: 0.8714 (t) cc_final: 0.8175 (m) REVERT: A 339 ARG cc_start: 0.6585 (mtp85) cc_final: 0.6250 (mtm180) REVERT: A 468 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7094 (tpp) REVERT: A 498 LEU cc_start: 0.7375 (tp) cc_final: 0.7103 (tp) REVERT: A 711 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.7000 (p0) REVERT: C 162 TYR cc_start: 0.3904 (OUTLIER) cc_final: 0.2933 (m-10) REVERT: C 286 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8398 (mt0) REVERT: C 517 ARG cc_start: 0.7176 (tpp-160) cc_final: 0.6858 (tpp-160) REVERT: C 524 ILE cc_start: 0.7784 (mp) cc_final: 0.7176 (mm) REVERT: C 528 MET cc_start: 0.8954 (mmm) cc_final: 0.8496 (mtt) REVERT: C 603 PHE cc_start: 0.8204 (m-10) cc_final: 0.7736 (m-80) REVERT: C 607 MET cc_start: 0.3306 (mmm) cc_final: 0.2015 (mmm) REVERT: D 81 PHE cc_start: 0.5703 (m-80) cc_final: 0.5251 (m-80) REVERT: D 404 MET cc_start: 0.5314 (tpt) cc_final: 0.4867 (tpt) REVERT: D 512 LEU cc_start: 0.7149 (tp) cc_final: 0.6760 (tp) REVERT: D 517 ARG cc_start: 0.8360 (tpt-90) cc_final: 0.7899 (ttt-90) REVERT: D 525 TYR cc_start: 0.7653 (m-80) cc_final: 0.7327 (m-80) outliers start: 44 outliers final: 35 residues processed: 248 average time/residue: 0.1164 time to fit residues: 47.0456 Evaluate side-chains 258 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 711 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 351 TRP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 65 optimal weight: 8.9990 chunk 122 optimal weight: 0.0000 chunk 186 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.182012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.132689 restraints weight = 35781.441| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.11 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19719 Z= 0.110 Angle : 0.638 13.075 26760 Z= 0.303 Chirality : 0.038 0.191 3031 Planarity : 0.003 0.047 3286 Dihedral : 3.968 31.109 2583 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.15 % Favored : 91.68 % Rotamer: Outliers : 1.98 % Allowed : 21.38 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.18), residues: 2343 helix: 1.41 (0.15), residues: 1236 sheet: -1.36 (0.62), residues: 65 loop : -2.69 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 535 TYR 0.019 0.001 TYR B 471 PHE 0.032 0.001 PHE D 601 TRP 0.017 0.001 TRP A 676 HIS 0.004 0.001 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.00250 (19719) covalent geometry : angle 0.63797 (26760) hydrogen bonds : bond 0.03211 ( 849) hydrogen bonds : angle 3.73497 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4902.68 seconds wall clock time: 85 minutes 18.00 seconds (5118.00 seconds total)