Starting phenix.real_space_refine on Tue Aug 26 14:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgw_43228/08_2025/8vgw_43228_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgw_43228/08_2025/8vgw_43228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vgw_43228/08_2025/8vgw_43228_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgw_43228/08_2025/8vgw_43228_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vgw_43228/08_2025/8vgw_43228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgw_43228/08_2025/8vgw_43228.map" } resolution = 3.9 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= 0.008 sd= 0.261 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 12159 2.51 5 N 3399 2.21 5 O 3654 1.98 5 H 18936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38283 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7205 Classifications: {'peptide': 461} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2127 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1904 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 113} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1525 Classifications: {'peptide': 101} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Chain: "E" Number of atoms: 7205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7205 Classifications: {'peptide': 461} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "F" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2127 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "G" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1904 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 113} Chain: "H" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1525 Classifications: {'peptide': 101} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Chain: "I" Number of atoms: 7205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 7205 Classifications: {'peptide': 461} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 435} Chain breaks: 1 Chain: "J" Number of atoms: 2127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2127 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1904 Classifications: {'peptide': 121} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1525 Classifications: {'peptide': 101} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain breaks: 1 Time building chain proxies: 5.88, per 1000 atoms: 0.15 Number of scatterers: 38283 At special positions: 0 Unit cell: (141.48, 150.12, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 O 3654 8.00 N 3399 7.00 C 12159 6.00 H 18936 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 158 " distance=2.02 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 117 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 258 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 403 " distance=2.02 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 376 " distance=2.04 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 558 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 167 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 158 " distance=2.02 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 117 " distance=2.03 Simple disulfide: pdb=" SG CYS E 180 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 190 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 258 " - pdb=" SG CYS E 292 " distance=2.04 Simple disulfide: pdb=" SG CYS E 338 " - pdb=" SG CYS E 403 " distance=2.02 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 376 " distance=2.04 Simple disulfide: pdb=" SG CYS E 459 " - pdb=" SG CYS F 565 " distance=2.03 Simple disulfide: pdb=" SG CYS F 558 " - pdb=" SG CYS F 564 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 44 " distance=2.03 Simple disulfide: pdb=" SG CYS I 89 " - pdb=" SG CYS I 167 " distance=2.03 Simple disulfide: pdb=" SG CYS I 96 " - pdb=" SG CYS I 158 " distance=2.02 Simple disulfide: pdb=" SG CYS I 101 " - pdb=" SG CYS I 117 " distance=2.03 Simple disulfide: pdb=" SG CYS I 180 " - pdb=" SG CYS I 209 " distance=2.03 Simple disulfide: pdb=" SG CYS I 190 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 258 " - pdb=" SG CYS I 292 " distance=2.04 Simple disulfide: pdb=" SG CYS I 338 " - pdb=" SG CYS I 403 " distance=2.03 Simple disulfide: pdb=" SG CYS I 345 " - pdb=" SG CYS I 376 " distance=2.03 Simple disulfide: pdb=" SG CYS I 459 " - pdb=" SG CYS J 565 " distance=2.03 Simple disulfide: pdb=" SG CYS J 558 " - pdb=" SG CYS J 564 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 2.80 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 46 sheets defined 20.2% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 removed outlier: 3.863A pdb=" N LYS A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 87 removed outlier: 4.452A pdb=" N ASP A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 3.611A pdb=" N LEU A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 314 removed outlier: 4.138A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.759A pdb=" N THR A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.651A pdb=" N LEU B 483 " --> pdb=" O PHE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 487 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 497 through 504 removed outlier: 4.126A pdb=" N ALA B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 557 removed outlier: 3.832A pdb=" N LEU B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 552 " --> pdb=" O ARG B 548 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 Processing helix chain 'B' and resid 587 through 592 removed outlier: 3.663A pdb=" N ASP B 592 " --> pdb=" O TRP B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 598 through 616 removed outlier: 3.917A pdb=" N GLY B 604 " --> pdb=" O GLN B 600 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 616 " --> pdb=" O GLN B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 624 removed outlier: 3.695A pdb=" N LEU B 623 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.801A pdb=" N GLY C 65 " --> pdb=" O PRO C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.673A pdb=" N ASP C 86 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 83 through 87' Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.513A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.872A pdb=" N LYS E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 86 removed outlier: 4.446A pdb=" N ASP E 72 " --> pdb=" O ASN E 68 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU E 86 " --> pdb=" O TRP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 295 through 314 removed outlier: 3.527A pdb=" N ILE E 308 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N HIS E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 438 removed outlier: 3.510A pdb=" N TRP E 437 " --> pdb=" O MET E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 442 removed outlier: 5.065A pdb=" N TYR E 442 " --> pdb=" O SER E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 439 through 442' Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'F' and resid 478 through 483 removed outlier: 3.976A pdb=" N LEU F 483 " --> pdb=" O PHE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 487 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 497 through 504 removed outlier: 4.085A pdb=" N ALA F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 557 removed outlier: 3.795A pdb=" N LEU F 536 " --> pdb=" O GLY F 532 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG F 539 " --> pdb=" O GLN F 535 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 541 " --> pdb=" O GLN F 537 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 548 " --> pdb=" O GLU F 544 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP F 549 " --> pdb=" O ARG F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 578 through 583 removed outlier: 3.545A pdb=" N ILE F 582 " --> pdb=" O ASN F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 592 removed outlier: 3.578A pdb=" N ASP F 592 " --> pdb=" O TRP F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 616 removed outlier: 3.930A pdb=" N GLY F 604 " --> pdb=" O GLN F 600 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 605 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN F 613 " --> pdb=" O SER F 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.656A pdb=" N GLY G 65 " --> pdb=" O PRO G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.745A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N THR G 87 " --> pdb=" O VAL G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'I' and resid 29 through 35 removed outlier: 3.899A pdb=" N LYS I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL I 35 " --> pdb=" O TYR I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 removed outlier: 3.740A pdb=" N SER I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 removed outlier: 3.530A pdb=" N LEU I 95 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 314 removed outlier: 3.536A pdb=" N ILE I 308 " --> pdb=" O GLN I 304 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 438 removed outlier: 4.100A pdb=" N ASN I 436 " --> pdb=" O ASP I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 466 removed outlier: 3.761A pdb=" N GLY I 465 " --> pdb=" O ARG I 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 483 removed outlier: 3.949A pdb=" N LEU J 483 " --> pdb=" O PHE J 479 " (cutoff:3.500A) Processing helix chain 'J' and resid 484 through 487 Processing helix chain 'J' and resid 489 through 495 removed outlier: 3.863A pdb=" N MET J 495 " --> pdb=" O GLY J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 504 removed outlier: 4.205A pdb=" N ALA J 501 " --> pdb=" O LEU J 497 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 557 removed outlier: 3.727A pdb=" N LEU J 536 " --> pdb=" O GLY J 532 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG J 539 " --> pdb=" O GLN J 535 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL J 540 " --> pdb=" O LEU J 536 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU J 541 " --> pdb=" O GLN J 537 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU J 552 " --> pdb=" O ARG J 548 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE J 555 " --> pdb=" O GLN J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 578 through 583 Processing helix chain 'J' and resid 587 through 592 Processing helix chain 'J' and resid 598 through 616 removed outlier: 3.868A pdb=" N GLY J 604 " --> pdb=" O GLN J 600 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU J 605 " --> pdb=" O ILE J 601 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN J 613 " --> pdb=" O SER J 609 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN J 616 " --> pdb=" O GLN J 612 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.703A pdb=" N GLY K 65 " --> pdb=" O PRO K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.777A pdb=" N THR K 87 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8 removed outlier: 4.347A pdb=" N VAL A 6 " --> pdb=" O THR B 566 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 4.023A pdb=" N ILE A 187 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 64 Processing sheet with id=AA6, first strand: chain 'A' and resid 129 through 136 removed outlier: 3.583A pdb=" N PHE A 136 " --> pdb=" O LYS A 115 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS A 115 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N GLU A 112 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N VAL A 106 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET A 114 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 104 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.542A pdb=" N THR A 164 " --> pdb=" O TYR A 393 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 221 through 223 removed outlier: 3.568A pdb=" N GLY A 409 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 233 through 235 removed outlier: 3.686A pdb=" N ILE A 401 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 254 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 379 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 342 " --> pdb=" O LYS A 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 264 through 269 removed outlier: 6.924A pdb=" N THR A 265 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.865A pdb=" N SER C 7 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.782A pdb=" N VAL C 89 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP C 50 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.095A pdb=" N LYS C 96 " --> pdb=" O PHE C 100D" (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE C 100D" --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.574A pdb=" N SER D 7 " --> pdb=" O SER D 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.132A pdb=" N LEU D 11 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 455 through 457 removed outlier: 4.589A pdb=" N VAL E 6 " --> pdb=" O THR F 566 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 15 through 17 removed outlier: 4.026A pdb=" N ILE E 187 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AC1, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AC2, first strand: chain 'E' and resid 61 through 64 Processing sheet with id=AC3, first strand: chain 'E' and resid 129 through 136 removed outlier: 3.611A pdb=" N PHE E 136 " --> pdb=" O LYS E 115 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 115 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 10.286A pdb=" N GLU E 112 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 11.634A pdb=" N VAL E 106 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET E 114 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA E 104 " --> pdb=" O MET E 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 164 through 165 removed outlier: 6.634A pdb=" N THR E 164 " --> pdb=" O TYR E 393 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 221 through 223 removed outlier: 3.530A pdb=" N GLY E 409 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 233 through 235 removed outlier: 3.518A pdb=" N VAL E 254 " --> pdb=" O ILE E 407 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR E 259 " --> pdb=" O HIS E 291 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS E 291 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS E 379 " --> pdb=" O PHE E 342 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE E 342 " --> pdb=" O LYS E 379 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 341 " --> pdb=" O CYS E 338 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 264 through 269 removed outlier: 6.900A pdb=" N THR E 265 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.841A pdb=" N SER G 7 " --> pdb=" O SER G 21 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.747A pdb=" N VAL G 89 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.105A pdb=" N LYS G 96 " --> pdb=" O PHE G 100D" (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE G 100D" --> pdb=" O LYS G 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.203A pdb=" N LEU H 11 " --> pdb=" O GLN H 105 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 5 through 8 removed outlier: 4.274A pdb=" N VAL I 6 " --> pdb=" O THR J 566 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 15 through 17 removed outlier: 3.507A pdb=" N LYS I 445 " --> pdb=" O LEU I 188 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE I 187 " --> pdb=" O VAL I 207 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL I 204 " --> pdb=" O LEU I 56 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 23 through 26 Processing sheet with id=AD7, first strand: chain 'I' and resid 37 through 38 Processing sheet with id=AD8, first strand: chain 'I' and resid 61 through 64 Processing sheet with id=AD9, first strand: chain 'I' and resid 129 through 136 removed outlier: 3.589A pdb=" N PHE I 136 " --> pdb=" O LYS I 115 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS I 115 " --> pdb=" O PHE I 136 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N GLU I 112 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N VAL I 106 " --> pdb=" O GLU I 112 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET I 114 " --> pdb=" O ALA I 104 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA I 104 " --> pdb=" O MET I 114 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 164 through 165 removed outlier: 6.546A pdb=" N THR I 164 " --> pdb=" O TYR I 393 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 221 through 223 removed outlier: 3.514A pdb=" N GLY I 409 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE I 401 " --> pdb=" O ARG I 260 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL I 254 " --> pdb=" O ILE I 407 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR I 259 " --> pdb=" O HIS I 291 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS I 291 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS I 379 " --> pdb=" O PHE I 342 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE I 342 " --> pdb=" O LYS I 379 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU I 341 " --> pdb=" O CYS I 338 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 233 through 235 Processing sheet with id=AE4, first strand: chain 'I' and resid 264 through 272 removed outlier: 6.907A pdb=" N THR I 265 " --> pdb=" O GLY I 281 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE I 271 " --> pdb=" O GLN I 275 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN I 275 " --> pdb=" O ILE I 271 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.715A pdb=" N SER K 7 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.392A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.160A pdb=" N LYS K 96 " --> pdb=" O PHE K 100D" (cutoff:3.500A) removed outlier: 8.134A pdb=" N PHE K 100D" --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.417A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.417A pdb=" N LEU L 11 " --> pdb=" O GLN L 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1725 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: 8.63 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 18930 1.04 - 1.24: 2745 1.24 - 1.45: 5895 1.45 - 1.65: 10947 1.65 - 1.85: 180 Bond restraints: 38697 Sorted by residual: bond pdb=" N ALA E 1 " pdb=" H1 ALA E 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" N ALA B 472 " pdb=" H1 ALA B 472 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ALA J 472 " pdb=" H1 ALA J 472 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU H 1 " pdb=" H1 GLU H 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLN K 1 " pdb=" H1 GLN K 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 38692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.77: 69711 7.77 - 15.55: 15 15.55 - 23.32: 0 23.32 - 31.09: 3 31.09 - 38.86: 6 Bond angle restraints: 69735 Sorted by residual: angle pdb=" C ARG I 471 " pdb=" CA ARG I 471 " pdb=" HA ARG I 471 " ideal model delta sigma weight residual 109.00 70.14 38.86 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C ARG E 471 " pdb=" CA ARG E 471 " pdb=" HA ARG E 471 " ideal model delta sigma weight residual 109.00 70.45 38.55 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C ARG A 471 " pdb=" CA ARG A 471 " pdb=" HA ARG A 471 " ideal model delta sigma weight residual 109.00 71.80 37.20 3.00e+00 1.11e-01 1.54e+02 angle pdb=" N ARG A 471 " pdb=" CA ARG A 471 " pdb=" HA ARG A 471 " ideal model delta sigma weight residual 110.00 75.71 34.29 3.00e+00 1.11e-01 1.31e+02 angle pdb=" N ARG E 471 " pdb=" CA ARG E 471 " pdb=" HA ARG E 471 " ideal model delta sigma weight residual 110.00 77.57 32.43 3.00e+00 1.11e-01 1.17e+02 ... (remaining 69730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 16465 17.58 - 35.16: 1393 35.16 - 52.74: 311 52.74 - 70.32: 120 70.32 - 87.89: 35 Dihedral angle restraints: 18324 sinusoidal: 10059 harmonic: 8265 Sorted by residual: dihedral pdb=" CA TYR E 10 " pdb=" C TYR E 10 " pdb=" N GLY E 11 " pdb=" CA GLY E 11 " ideal model delta harmonic sigma weight residual 180.00 136.42 43.58 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CA TYR E 9 " pdb=" C TYR E 9 " pdb=" N TYR E 10 " pdb=" CA TYR E 10 " ideal model delta harmonic sigma weight residual 180.00 -140.94 -39.06 0 5.00e+00 4.00e-02 6.10e+01 dihedral pdb=" CA PRO E 451 " pdb=" C PRO E 451 " pdb=" N LEU E 452 " pdb=" CA LEU E 452 " ideal model delta harmonic sigma weight residual -180.00 -143.92 -36.08 0 5.00e+00 4.00e-02 5.21e+01 ... (remaining 18321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2698 0.086 - 0.172: 265 0.172 - 0.259: 1 0.259 - 0.345: 0 0.345 - 0.431: 3 Chirality restraints: 2967 Sorted by residual: chirality pdb=" CA ARG E 471 " pdb=" N ARG E 471 " pdb=" C ARG E 471 " pdb=" CB ARG E 471 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA ARG I 471 " pdb=" N ARG I 471 " pdb=" C ARG I 471 " pdb=" CB ARG I 471 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA ARG A 471 " pdb=" N ARG A 471 " pdb=" C ARG A 471 " pdb=" CB ARG A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 2964 not shown) Planarity restraints: 5787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 10 " -0.041 2.00e-02 2.50e+03 1.66e-02 8.29e+00 pdb=" CG TYR E 10 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR E 10 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR E 10 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR E 10 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 10 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 10 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 10 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TYR E 10 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR E 10 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR E 10 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR E 10 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 452 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C LEU A 452 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU A 452 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 453 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 583 " -0.020 2.00e-02 2.50e+03 1.30e-02 6.79e+00 pdb=" CG TRP F 583 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP F 583 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP F 583 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP F 583 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 583 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 583 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 583 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 583 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 583 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP F 583 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP F 583 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP F 583 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 583 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 583 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP F 583 " -0.000 2.00e-02 2.50e+03 ... (remaining 5784 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3408 2.23 - 2.82: 82731 2.82 - 3.42: 95900 3.42 - 4.01: 132576 4.01 - 4.60: 204144 Nonbonded interactions: 518759 Sorted by model distance: nonbonded pdb=" O ARG A 470 " pdb=" H ALA F 622 " model vdw 1.642 2.450 nonbonded pdb=" O ARG E 470 " pdb=" H ALA J 622 " model vdw 1.645 2.450 nonbonded pdb=" H ILE E 177 " pdb=" O ILE E 213 " model vdw 1.691 2.450 nonbonded pdb="HH22 ARG H 54 " pdb=" O PRO H 59 " model vdw 1.700 2.450 nonbonded pdb=" H ILE A 177 " pdb=" O ILE A 213 " model vdw 1.707 2.450 ... (remaining 518754 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } 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 group one per residue 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: 1.730 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: 0.180 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.010 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.004 0.050 19803 Z= 0.193 Angle : 0.821 10.801 26910 Z= 0.455 Chirality : 0.050 0.431 2967 Planarity : 0.005 0.059 3459 Dihedral : 13.710 87.894 7239 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.71 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.17), residues: 2415 helix: -1.82 (0.24), residues: 369 sheet: -0.98 (0.19), residues: 744 loop : -1.35 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 469 TYR 0.039 0.002 TYR E 10 PHE 0.011 0.002 PHE F 482 TRP 0.044 0.002 TRP F 583 HIS 0.005 0.001 HIS I 334 Details of bonding type rmsd covalent geometry : bond 0.00418 (19761) covalent geometry : angle 0.81952 (26826) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.25136 ( 84) hydrogen bonds : bond 0.26580 ( 658) hydrogen bonds : angle 9.81151 ( 1725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLN cc_start: 0.8232 (mp10) cc_final: 0.7629 (mt0) REVERT: A 349 ASN cc_start: 0.7862 (m110) cc_final: 0.7469 (t0) REVERT: A 404 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7301 (mtm110) REVERT: A 449 ILE cc_start: 0.7108 (mt) cc_final: 0.6711 (tt) REVERT: B 505 LEU cc_start: 0.7568 (mt) cc_final: 0.7314 (mt) REVERT: C 13 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7681 (mmmt) REVERT: C 16 GLU cc_start: 0.7985 (pt0) cc_final: 0.7072 (tt0) REVERT: C 68 THR cc_start: 0.9451 (t) cc_final: 0.9237 (m) REVERT: D 27 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7424 (pt0) REVERT: D 86 TYR cc_start: 0.7641 (m-80) cc_final: 0.7284 (m-80) REVERT: D 91 TYR cc_start: 0.7525 (m-80) cc_final: 0.7064 (m-80) REVERT: E 17 GLU cc_start: 0.6239 (mm-30) cc_final: 0.5851 (mt-10) REVERT: E 70 MET cc_start: 0.8645 (mtm) cc_final: 0.8428 (mtp) REVERT: E 256 ILE cc_start: 0.9089 (mt) cc_final: 0.8743 (tt) REVERT: E 275 GLN cc_start: 0.8164 (mp10) cc_final: 0.7831 (mt0) REVERT: E 349 ASN cc_start: 0.7766 (m110) cc_final: 0.7414 (t0) REVERT: E 449 ILE cc_start: 0.7262 (mt) cc_final: 0.6753 (tt) REVERT: F 585 ASN cc_start: 0.6504 (m-40) cc_final: 0.6234 (m110) REVERT: G 13 LYS cc_start: 0.8655 (mmtm) cc_final: 0.7942 (mmmt) REVERT: G 16 GLU cc_start: 0.8140 (pt0) cc_final: 0.7360 (tt0) REVERT: G 68 THR cc_start: 0.9424 (t) cc_final: 0.9165 (m) REVERT: G 96 LYS cc_start: 0.8033 (pttp) cc_final: 0.7823 (tttm) REVERT: I 17 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5877 (mt-10) REVERT: I 72 ASP cc_start: 0.8638 (m-30) cc_final: 0.8278 (m-30) REVERT: I 76 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7534 (mp0) REVERT: I 79 ILE cc_start: 0.7602 (tp) cc_final: 0.7381 (pt) REVERT: I 208 GLN cc_start: 0.8312 (mt0) cc_final: 0.8020 (mm-40) REVERT: I 349 ASN cc_start: 0.7866 (m110) cc_final: 0.7567 (t0) REVERT: I 390 ARG cc_start: 0.6918 (tpm170) cc_final: 0.6483 (mpp-170) REVERT: I 404 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.6926 (ptt-90) REVERT: J 548 ARG cc_start: 0.7731 (tpt170) cc_final: 0.7303 (ttm-80) REVERT: J 601 ILE cc_start: 0.6113 (mt) cc_final: 0.5899 (mm) REVERT: K 13 LYS cc_start: 0.8578 (mmtm) cc_final: 0.7853 (mmmt) REVERT: K 16 GLU cc_start: 0.8072 (pt0) cc_final: 0.7349 (tt0) REVERT: K 82 ARG cc_start: 0.8890 (mpp80) cc_final: 0.8527 (mtt-85) REVERT: K 105 ARG cc_start: 0.7433 (mtm110) cc_final: 0.7065 (mtp180) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.3688 time to fit residues: 220.9996 Evaluate side-chains 198 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.0270 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 108 ASN A 386 GLN B 567 ASN C 97 ASN E 37 ASN E 73 GLN E 108 ASN I 36 HIS I 108 ASN I 251 HIS J 567 ASN L 27 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.165610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145469 restraints weight = 663136.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.148414 restraints weight = 407149.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.147971 restraints weight = 323839.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.148355 restraints weight = 353823.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148446 restraints weight = 326355.954| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19803 Z= 0.130 Angle : 0.627 9.569 26910 Z= 0.337 Chirality : 0.046 0.441 2967 Planarity : 0.005 0.046 3459 Dihedral : 6.222 48.290 2673 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 1.36 % Allowed : 7.09 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2415 helix: -1.01 (0.25), residues: 375 sheet: -0.77 (0.19), residues: 750 loop : -1.36 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.034 0.001 TYR E 10 PHE 0.014 0.001 PHE E 23 TRP 0.024 0.001 TRP F 583 HIS 0.012 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00284 (19761) covalent geometry : angle 0.62123 (26826) SS BOND : bond 0.00653 ( 42) SS BOND : angle 1.59904 ( 84) hydrogen bonds : bond 0.05396 ( 658) hydrogen bonds : angle 6.65296 ( 1725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLN cc_start: 0.8147 (tp40) cc_final: 0.7181 (tm-30) REVERT: A 95 LEU cc_start: 0.8404 (mt) cc_final: 0.7971 (tt) REVERT: A 275 GLN cc_start: 0.8314 (mp10) cc_final: 0.7559 (mt0) REVERT: A 349 ASN cc_start: 0.7845 (m110) cc_final: 0.7300 (t0) REVERT: A 404 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7386 (ttm110) REVERT: B 544 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: B 563 ILE cc_start: 0.8875 (mm) cc_final: 0.8668 (mt) REVERT: C 13 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8042 (mmmt) REVERT: C 82 ARG cc_start: 0.9127 (mpp80) cc_final: 0.8795 (mtt-85) REVERT: C 97 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8373 (p0) REVERT: D 27 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7414 (pt0) REVERT: D 82 ASP cc_start: 0.6835 (m-30) cc_final: 0.6346 (m-30) REVERT: D 91 TYR cc_start: 0.7721 (m-80) cc_final: 0.7243 (m-80) REVERT: E 17 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6149 (mt-10) REVERT: E 95 LEU cc_start: 0.8555 (mt) cc_final: 0.8186 (tt) REVERT: E 275 GLN cc_start: 0.8316 (mp10) cc_final: 0.7862 (mt0) REVERT: E 349 ASN cc_start: 0.7613 (m110) cc_final: 0.7230 (t0) REVERT: E 384 MET cc_start: 0.5604 (mmm) cc_final: 0.5267 (mmm) REVERT: F 544 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7896 (tp30) REVERT: G 13 LYS cc_start: 0.8605 (mmtm) cc_final: 0.8210 (mmmt) REVERT: G 96 LYS cc_start: 0.7988 (pttp) cc_final: 0.7764 (tttm) REVERT: I 17 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6096 (mt-10) REVERT: I 72 ASP cc_start: 0.8241 (m-30) cc_final: 0.7877 (m-30) REVERT: I 74 MET cc_start: 0.8343 (ttp) cc_final: 0.8015 (ttt) REVERT: I 76 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7365 (mp0) REVERT: I 95 LEU cc_start: 0.8306 (mt) cc_final: 0.7961 (tt) REVERT: I 208 GLN cc_start: 0.8354 (mt0) cc_final: 0.7983 (mm-40) REVERT: I 349 ASN cc_start: 0.7853 (m110) cc_final: 0.7463 (t0) REVERT: I 390 ARG cc_start: 0.6781 (tpm170) cc_final: 0.6571 (mpp-170) REVERT: J 548 ARG cc_start: 0.7585 (tpt170) cc_final: 0.6791 (ttm-80) REVERT: J 570 TRP cc_start: 0.7450 (t-100) cc_final: 0.7199 (t-100) REVERT: J 594 GLU cc_start: 0.5862 (mt-10) cc_final: 0.5537 (mt-10) REVERT: J 601 ILE cc_start: 0.6503 (mt) cc_final: 0.6265 (mm) REVERT: K 13 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8065 (mmmt) outliers start: 29 outliers final: 14 residues processed: 253 average time/residue: 0.2938 time to fit residues: 112.7899 Evaluate side-chains 212 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 386 GLN Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN J 567 ASN L 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.133428 restraints weight = 689963.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.136102 restraints weight = 423602.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.135755 restraints weight = 343960.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136308 restraints weight = 362632.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.136288 restraints weight = 339870.399| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19803 Z= 0.146 Angle : 0.611 9.702 26910 Z= 0.326 Chirality : 0.046 0.448 2967 Planarity : 0.004 0.042 3459 Dihedral : 5.886 41.746 2673 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.12 % Favored : 92.80 % Rotamer: Outliers : 1.36 % Allowed : 9.06 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.17), residues: 2415 helix: -0.68 (0.26), residues: 381 sheet: -0.84 (0.19), residues: 759 loop : -1.50 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.035 0.002 TYR E 10 PHE 0.012 0.001 PHE I 351 TRP 0.025 0.001 TRP F 583 HIS 0.004 0.001 HIS I 178 Details of bonding type rmsd covalent geometry : bond 0.00337 (19761) covalent geometry : angle 0.60585 (26826) SS BOND : bond 0.00496 ( 42) SS BOND : angle 1.60099 ( 84) hydrogen bonds : bond 0.04569 ( 658) hydrogen bonds : angle 5.99684 ( 1725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8528 (mt) cc_final: 0.8083 (tt) REVERT: A 349 ASN cc_start: 0.7921 (m110) cc_final: 0.7316 (t0) REVERT: A 404 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7231 (ttm110) REVERT: B 563 ILE cc_start: 0.9021 (mm) cc_final: 0.8814 (mt) REVERT: C 13 LYS cc_start: 0.8510 (mmtm) cc_final: 0.8073 (mmmt) REVERT: D 27 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7372 (pt0) REVERT: D 91 TYR cc_start: 0.7626 (m-80) cc_final: 0.7062 (m-10) REVERT: E 17 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6112 (mt-10) REVERT: E 275 GLN cc_start: 0.8377 (mp10) cc_final: 0.7883 (mt0) REVERT: E 349 ASN cc_start: 0.7944 (m110) cc_final: 0.7445 (t0) REVERT: E 390 ARG cc_start: 0.7150 (ttm170) cc_final: 0.6167 (mpt180) REVERT: G 13 LYS cc_start: 0.8569 (mmtm) cc_final: 0.8258 (mmmt) REVERT: G 96 LYS cc_start: 0.8182 (pttp) cc_final: 0.7799 (tttm) REVERT: I 17 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6179 (mt-10) REVERT: I 72 ASP cc_start: 0.8190 (m-30) cc_final: 0.7893 (m-30) REVERT: I 76 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7521 (mp0) REVERT: I 79 ILE cc_start: 0.7626 (tp) cc_final: 0.7117 (pt) REVERT: I 95 LEU cc_start: 0.8523 (mt) cc_final: 0.8113 (tt) REVERT: I 208 GLN cc_start: 0.8567 (mt0) cc_final: 0.8202 (tp-100) REVERT: I 390 ARG cc_start: 0.6814 (tpm170) cc_final: 0.6534 (mpp-170) REVERT: J 505 LEU cc_start: 0.7885 (mt) cc_final: 0.7659 (mt) REVERT: J 548 ARG cc_start: 0.7427 (tpt170) cc_final: 0.6761 (ttm-80) REVERT: K 13 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8188 (mmmt) outliers start: 29 outliers final: 21 residues processed: 219 average time/residue: 0.3006 time to fit residues: 99.2136 Evaluate side-chains 201 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain J residue 592 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN G 35 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN J 567 ASN L 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125443 restraints weight = 705628.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128147 restraints weight = 439339.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127506 restraints weight = 359273.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128035 restraints weight = 374228.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.127836 restraints weight = 353466.708| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 19803 Z= 0.246 Angle : 0.708 9.865 26910 Z= 0.380 Chirality : 0.049 0.448 2967 Planarity : 0.005 0.046 3459 Dihedral : 6.311 44.336 2673 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.06 % Rotamer: Outliers : 2.49 % Allowed : 10.80 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.17), residues: 2415 helix: -0.67 (0.27), residues: 399 sheet: -1.02 (0.19), residues: 762 loop : -1.97 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 545 TYR 0.039 0.002 TYR E 10 PHE 0.025 0.002 PHE I 351 TRP 0.027 0.002 TRP F 583 HIS 0.007 0.002 HIS I 178 Details of bonding type rmsd covalent geometry : bond 0.00589 (19761) covalent geometry : angle 0.70097 (26826) SS BOND : bond 0.00596 ( 42) SS BOND : angle 1.91312 ( 84) hydrogen bonds : bond 0.04751 ( 658) hydrogen bonds : angle 6.03591 ( 1725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8578 (mt) cc_final: 0.8122 (tt) REVERT: A 140 ASP cc_start: 0.4759 (OUTLIER) cc_final: 0.4484 (m-30) REVERT: C 13 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8180 (mmmt) REVERT: E 17 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6308 (mt-10) REVERT: E 140 ASP cc_start: 0.4588 (OUTLIER) cc_final: 0.4146 (m-30) REVERT: E 275 GLN cc_start: 0.8470 (mp10) cc_final: 0.7799 (mt0) REVERT: E 449 ILE cc_start: 0.7385 (mt) cc_final: 0.7177 (tt) REVERT: G 13 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8328 (mmmt) REVERT: G 96 LYS cc_start: 0.8322 (pttp) cc_final: 0.8076 (tttp) REVERT: I 17 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6507 (mt-10) REVERT: I 76 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7344 (mp0) REVERT: I 79 ILE cc_start: 0.7730 (tp) cc_final: 0.7223 (pt) REVERT: I 95 LEU cc_start: 0.8620 (mt) cc_final: 0.8413 (tt) REVERT: I 140 ASP cc_start: 0.4637 (OUTLIER) cc_final: 0.4146 (m-30) REVERT: I 208 GLN cc_start: 0.8700 (mt0) cc_final: 0.8310 (tt0) REVERT: I 390 ARG cc_start: 0.6938 (tpm170) cc_final: 0.6699 (mpp-170) REVERT: J 548 ARG cc_start: 0.7470 (tpt170) cc_final: 0.6882 (ttm-80) REVERT: K 13 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8372 (mmmt) REVERT: K 82 ARG cc_start: 0.9130 (mpp80) cc_final: 0.8782 (mtt-85) outliers start: 53 outliers final: 39 residues processed: 225 average time/residue: 0.3037 time to fit residues: 103.0797 Evaluate side-chains 217 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 559 SER Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 322 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain J residue 616 ASN Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain L residue 105 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 154 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 120 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 567 ASN G 58 ASN J 551 GLN J 567 ASN L 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129303 restraints weight = 697322.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131889 restraints weight = 433040.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131657 restraints weight = 351290.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.132022 restraints weight = 370763.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131938 restraints weight = 340190.637| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19803 Z= 0.132 Angle : 0.594 9.739 26910 Z= 0.316 Chirality : 0.046 0.450 2967 Planarity : 0.004 0.048 3459 Dihedral : 5.837 41.432 2673 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 1.97 % Allowed : 12.16 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.17), residues: 2415 helix: -0.49 (0.27), residues: 399 sheet: -1.04 (0.18), residues: 777 loop : -1.84 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 404 TYR 0.034 0.001 TYR E 10 PHE 0.011 0.001 PHE I 351 TRP 0.025 0.001 TRP F 583 HIS 0.003 0.001 HIS I 334 Details of bonding type rmsd covalent geometry : bond 0.00307 (19761) covalent geometry : angle 0.58984 (26826) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.40219 ( 84) hydrogen bonds : bond 0.03930 ( 658) hydrogen bonds : angle 5.64535 ( 1725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8507 (mt) cc_final: 0.8064 (tt) REVERT: A 167 CYS cc_start: 0.6747 (OUTLIER) cc_final: 0.5996 (m) REVERT: C 13 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8260 (mmmt) REVERT: D 91 TYR cc_start: 0.7692 (m-80) cc_final: 0.7241 (m-80) REVERT: E 17 GLU cc_start: 0.6883 (mm-30) cc_final: 0.6331 (mt-10) REVERT: E 349 ASN cc_start: 0.7827 (m110) cc_final: 0.7074 (t0) REVERT: E 390 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6451 (mpp-170) REVERT: G 13 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8268 (mmmt) REVERT: G 96 LYS cc_start: 0.8170 (pttp) cc_final: 0.7896 (tttp) REVERT: I 17 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6388 (mt-10) REVERT: I 76 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7325 (mp0) REVERT: I 79 ILE cc_start: 0.7874 (tp) cc_final: 0.7350 (pt) REVERT: I 95 LEU cc_start: 0.8552 (mt) cc_final: 0.8268 (tt) REVERT: I 208 GLN cc_start: 0.8557 (mt0) cc_final: 0.8302 (tt0) REVERT: I 349 ASN cc_start: 0.7747 (m-40) cc_final: 0.7077 (t0) REVERT: I 390 ARG cc_start: 0.6915 (tpm170) cc_final: 0.6675 (mpp-170) REVERT: J 548 ARG cc_start: 0.7401 (tpt170) cc_final: 0.6798 (ttm-80) REVERT: K 13 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8310 (mmmt) REVERT: K 82 ARG cc_start: 0.9102 (mpp80) cc_final: 0.8785 (mtt-85) outliers start: 42 outliers final: 34 residues processed: 221 average time/residue: 0.2864 time to fit residues: 96.1226 Evaluate side-chains 216 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 564 CYS Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 418 THR Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 143 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 163 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 ASN J 567 ASN L 105 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130389 restraints weight = 694529.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132994 restraints weight = 423075.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132544 restraints weight = 350956.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132898 restraints weight = 371127.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.132939 restraints weight = 343827.197| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19803 Z= 0.126 Angle : 0.572 9.538 26910 Z= 0.303 Chirality : 0.045 0.449 2967 Planarity : 0.004 0.064 3459 Dihedral : 5.577 41.781 2673 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.95 % Favored : 91.97 % Rotamer: Outliers : 2.11 % Allowed : 12.63 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.17), residues: 2415 helix: -0.26 (0.27), residues: 393 sheet: -1.07 (0.18), residues: 780 loop : -1.84 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 61 TYR 0.034 0.001 TYR E 10 PHE 0.011 0.001 PHE I 351 TRP 0.024 0.001 TRP F 583 HIS 0.003 0.001 HIS I 334 Details of bonding type rmsd covalent geometry : bond 0.00292 (19761) covalent geometry : angle 0.56834 (26826) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.28339 ( 84) hydrogen bonds : bond 0.03684 ( 658) hydrogen bonds : angle 5.42462 ( 1725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8520 (mt) cc_final: 0.8100 (tt) REVERT: A 167 CYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6230 (m) REVERT: A 301 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7505 (t0) REVERT: A 349 ASN cc_start: 0.7951 (m-40) cc_final: 0.7049 (t0) REVERT: C 13 LYS cc_start: 0.8442 (mmtm) cc_final: 0.8143 (mmmt) REVERT: D 91 TYR cc_start: 0.7719 (m-80) cc_final: 0.7384 (m-80) REVERT: E 17 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6316 (mt-10) REVERT: E 275 GLN cc_start: 0.8497 (mp10) cc_final: 0.7756 (mt0) REVERT: E 349 ASN cc_start: 0.7825 (m110) cc_final: 0.7041 (t0) REVERT: E 390 ARG cc_start: 0.6962 (ttm170) cc_final: 0.6465 (mpp-170) REVERT: G 13 LYS cc_start: 0.8656 (mmtm) cc_final: 0.8375 (mmmt) REVERT: G 96 LYS cc_start: 0.8092 (pttp) cc_final: 0.7835 (tttp) REVERT: I 17 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6467 (mt-10) REVERT: I 76 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7560 (mp0) REVERT: I 79 ILE cc_start: 0.7815 (tp) cc_final: 0.7476 (mt) REVERT: I 95 LEU cc_start: 0.8588 (mt) cc_final: 0.8336 (tt) REVERT: I 349 ASN cc_start: 0.7872 (m-40) cc_final: 0.7175 (t0) REVERT: I 390 ARG cc_start: 0.6789 (tpm170) cc_final: 0.6520 (mpp-170) REVERT: J 548 ARG cc_start: 0.7396 (tpt170) cc_final: 0.6916 (ttm-80) REVERT: K 13 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8303 (mmmt) REVERT: K 82 ARG cc_start: 0.9099 (mpp80) cc_final: 0.8785 (mtt-85) outliers start: 45 outliers final: 40 residues processed: 225 average time/residue: 0.3060 time to fit residues: 103.9457 Evaluate side-chains 220 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 238 ASN Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 418 THR Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 564 CYS Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 322 ASN Chi-restraints excluded: chain I residue 405 SER Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 72 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 113 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 3 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 567 ASN L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135234 restraints weight = 688720.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.138188 restraints weight = 419117.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.137314 restraints weight = 334806.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137729 restraints weight = 359162.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137455 restraints weight = 335088.199| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19803 Z= 0.190 Angle : 0.620 9.305 26910 Z= 0.331 Chirality : 0.047 0.447 2967 Planarity : 0.004 0.041 3459 Dihedral : 5.764 43.654 2673 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.06 % Rotamer: Outliers : 2.72 % Allowed : 13.00 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.17), residues: 2415 helix: -0.29 (0.27), residues: 393 sheet: -1.17 (0.19), residues: 765 loop : -1.96 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 404 TYR 0.037 0.002 TYR E 10 PHE 0.017 0.002 PHE I 351 TRP 0.026 0.002 TRP F 583 HIS 0.005 0.001 HIS I 334 Details of bonding type rmsd covalent geometry : bond 0.00450 (19761) covalent geometry : angle 0.61512 (26826) SS BOND : bond 0.00456 ( 42) SS BOND : angle 1.47062 ( 84) hydrogen bonds : bond 0.04011 ( 658) hydrogen bonds : angle 5.54009 ( 1725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 188 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8579 (mt) cc_final: 0.8071 (tt) REVERT: A 167 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6452 (m) REVERT: A 301 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7594 (t0) REVERT: C 13 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8193 (mmmt) REVERT: E 390 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6522 (mpp-170) REVERT: G 13 LYS cc_start: 0.8635 (mmtm) cc_final: 0.8366 (mmmt) REVERT: H 63 SER cc_start: 0.8404 (OUTLIER) cc_final: 0.7764 (p) REVERT: I 17 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6582 (mt-10) REVERT: I 76 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7574 (mp0) REVERT: I 79 ILE cc_start: 0.7896 (tp) cc_final: 0.7527 (mt) REVERT: I 95 LEU cc_start: 0.8641 (mt) cc_final: 0.8315 (tt) REVERT: I 349 ASN cc_start: 0.7873 (m-40) cc_final: 0.7189 (t0) REVERT: I 390 ARG cc_start: 0.6972 (tpm170) cc_final: 0.6701 (mpp-170) REVERT: J 548 ARG cc_start: 0.7499 (tpt170) cc_final: 0.6931 (ttm-80) REVERT: K 13 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8354 (mmmt) REVERT: K 82 ARG cc_start: 0.9196 (mpp80) cc_final: 0.8805 (mtt-85) outliers start: 58 outliers final: 46 residues processed: 235 average time/residue: 0.3068 time to fit residues: 108.5016 Evaluate side-chains 231 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 564 CYS Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 322 ASN Chi-restraints excluded: chain I residue 405 SER Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 72 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 184 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 ASN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN E 238 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 567 ASN K 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.126190 restraints weight = 705310.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128775 restraints weight = 434462.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128125 restraints weight = 353168.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.128564 restraints weight = 376291.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.128461 restraints weight = 346823.197| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19803 Z= 0.180 Angle : 0.619 9.380 26910 Z= 0.331 Chirality : 0.047 0.448 2967 Planarity : 0.004 0.040 3459 Dihedral : 5.798 43.366 2673 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.86 % Favored : 91.06 % Rotamer: Outliers : 2.72 % Allowed : 13.29 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.17), residues: 2415 helix: -0.33 (0.27), residues: 393 sheet: -1.24 (0.18), residues: 771 loop : -2.01 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.036 0.002 TYR E 10 PHE 0.016 0.002 PHE I 351 TRP 0.026 0.002 TRP F 583 HIS 0.005 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00428 (19761) covalent geometry : angle 0.61411 (26826) SS BOND : bond 0.00486 ( 42) SS BOND : angle 1.49177 ( 84) hydrogen bonds : bond 0.03971 ( 658) hydrogen bonds : angle 5.55769 ( 1725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8646 (mt) cc_final: 0.8182 (tt) REVERT: A 167 CYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6763 (m) REVERT: A 301 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7444 (t0) REVERT: C 13 LYS cc_start: 0.8479 (mmtm) cc_final: 0.8188 (mmmt) REVERT: E 17 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6471 (mt-10) REVERT: G 13 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8426 (mmmt) REVERT: H 63 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7742 (p) REVERT: I 17 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6735 (mt-10) REVERT: I 76 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7566 (mp0) REVERT: I 79 ILE cc_start: 0.7860 (tp) cc_final: 0.7469 (mt) REVERT: I 95 LEU cc_start: 0.8570 (mt) cc_final: 0.8272 (tt) REVERT: I 349 ASN cc_start: 0.7865 (m-40) cc_final: 0.7182 (t0) REVERT: I 390 ARG cc_start: 0.6982 (tpm170) cc_final: 0.6614 (mpp-170) REVERT: J 548 ARG cc_start: 0.7449 (tpt170) cc_final: 0.6906 (ttm-80) REVERT: K 13 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8273 (mmmt) REVERT: K 82 ARG cc_start: 0.9177 (mpp80) cc_final: 0.8773 (mtt-85) outliers start: 58 outliers final: 53 residues processed: 234 average time/residue: 0.2986 time to fit residues: 105.2971 Evaluate side-chains 238 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 37 ASN Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 564 CYS Chi-restraints excluded: chain F residue 573 SER Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 322 ASN Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 405 SER Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 76 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 211 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 234 optimal weight: 0.0050 chunk 145 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN J 567 ASN K 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.161570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.139879 restraints weight = 677018.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.143326 restraints weight = 405975.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142410 restraints weight = 315471.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.142842 restraints weight = 331739.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142857 restraints weight = 315118.600| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19803 Z= 0.107 Angle : 0.556 9.566 26910 Z= 0.294 Chirality : 0.045 0.450 2967 Planarity : 0.004 0.041 3459 Dihedral : 5.434 40.608 2673 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 1.88 % Allowed : 14.37 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.17), residues: 2415 helix: -0.13 (0.27), residues: 393 sheet: -0.91 (0.19), residues: 732 loop : -1.89 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 82A TYR 0.036 0.001 TYR E 10 PHE 0.009 0.001 PHE I 23 TRP 0.025 0.001 TRP F 583 HIS 0.002 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00246 (19761) covalent geometry : angle 0.55247 (26826) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.29539 ( 84) hydrogen bonds : bond 0.03419 ( 658) hydrogen bonds : angle 5.28740 ( 1725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8432 (mt) cc_final: 0.8073 (tt) REVERT: A 167 CYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6414 (m) REVERT: A 172 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: A 301 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7491 (t0) REVERT: A 349 ASN cc_start: 0.7783 (m-40) cc_final: 0.6841 (t0) REVERT: C 13 LYS cc_start: 0.8427 (mmtm) cc_final: 0.8193 (mmmt) REVERT: D 91 TYR cc_start: 0.7672 (m-80) cc_final: 0.7307 (m-80) REVERT: E 17 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6415 (mt-10) REVERT: E 83 ASP cc_start: 0.8165 (t0) cc_final: 0.7815 (t0) REVERT: E 95 LEU cc_start: 0.8577 (mt) cc_final: 0.8350 (tt) REVERT: E 349 ASN cc_start: 0.7822 (m110) cc_final: 0.7075 (t0) REVERT: E 390 ARG cc_start: 0.6907 (ttm170) cc_final: 0.6529 (mpp-170) REVERT: G 13 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8309 (mmmt) REVERT: H 63 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7798 (p) REVERT: I 17 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6554 (mt-10) REVERT: I 76 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7373 (mp0) REVERT: I 95 LEU cc_start: 0.8523 (mt) cc_final: 0.8315 (tt) REVERT: I 349 ASN cc_start: 0.7857 (m-40) cc_final: 0.7146 (t0) REVERT: I 390 ARG cc_start: 0.6895 (tpm170) cc_final: 0.6628 (mpp-170) REVERT: J 548 ARG cc_start: 0.7454 (tpt170) cc_final: 0.6985 (ttm-80) REVERT: K 13 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8306 (mmmt) REVERT: K 82 ARG cc_start: 0.9133 (mpp80) cc_final: 0.8860 (mtt-85) outliers start: 40 outliers final: 34 residues processed: 223 average time/residue: 0.2894 time to fit residues: 98.1299 Evaluate side-chains 221 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 564 CYS Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain I residue 37 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 405 SER Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 72 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 56 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN J 567 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.128215 restraints weight = 695981.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.131305 restraints weight = 430180.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130405 restraints weight = 347674.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130812 restraints weight = 370505.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130743 restraints weight = 346045.407| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19803 Z= 0.158 Angle : 0.593 9.370 26910 Z= 0.315 Chirality : 0.046 0.448 2967 Planarity : 0.004 0.071 3459 Dihedral : 5.544 42.875 2673 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.99 % Favored : 90.93 % Rotamer: Outliers : 1.97 % Allowed : 14.65 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.17), residues: 2415 helix: -0.14 (0.27), residues: 393 sheet: -1.08 (0.19), residues: 765 loop : -1.94 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 61 TYR 0.035 0.001 TYR E 10 PHE 0.015 0.001 PHE I 351 TRP 0.025 0.001 TRP F 583 HIS 0.004 0.001 HIS I 334 Details of bonding type rmsd covalent geometry : bond 0.00373 (19761) covalent geometry : angle 0.58825 (26826) SS BOND : bond 0.00449 ( 42) SS BOND : angle 1.41653 ( 84) hydrogen bonds : bond 0.03726 ( 658) hydrogen bonds : angle 5.36486 ( 1725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8594 (mt) cc_final: 0.8208 (tt) REVERT: A 167 CYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6613 (m) REVERT: A 172 PHE cc_start: 0.8803 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 301 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7527 (t0) REVERT: C 13 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8207 (mmmt) REVERT: E 17 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6386 (mt-10) REVERT: E 95 LEU cc_start: 0.8642 (mt) cc_final: 0.8344 (tt) REVERT: E 349 ASN cc_start: 0.7787 (m110) cc_final: 0.6945 (t0) REVERT: G 13 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8350 (mmmt) REVERT: H 63 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7704 (p) REVERT: I 76 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7600 (mp0) REVERT: I 79 ILE cc_start: 0.7877 (tp) cc_final: 0.7524 (mt) REVERT: I 95 LEU cc_start: 0.8614 (mt) cc_final: 0.8361 (tt) REVERT: I 349 ASN cc_start: 0.7865 (m-40) cc_final: 0.7163 (t0) REVERT: I 390 ARG cc_start: 0.6979 (tpm170) cc_final: 0.6663 (mpp-170) REVERT: J 548 ARG cc_start: 0.7510 (tpt170) cc_final: 0.6936 (ttm-80) REVERT: K 13 LYS cc_start: 0.8692 (mmtm) cc_final: 0.8307 (mmmt) REVERT: K 82 ARG cc_start: 0.9196 (mpp80) cc_final: 0.8816 (mtt-85) outliers start: 42 outliers final: 36 residues processed: 221 average time/residue: 0.3051 time to fit residues: 101.9979 Evaluate side-chains 221 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 377 ARG Chi-restraints excluded: chain B residue 583 TRP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain F residue 564 CYS Chi-restraints excluded: chain F residue 583 TRP Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 63 SER Chi-restraints excluded: chain H residue 72 ASN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 158 CYS Chi-restraints excluded: chain I residue 233 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 405 SER Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain J residue 475 ILE Chi-restraints excluded: chain J residue 567 ASN Chi-restraints excluded: chain J residue 592 ASP Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 72 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 238 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** I 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 567 ASN L 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.152219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130580 restraints weight = 694206.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.133130 restraints weight = 426405.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.132637 restraints weight = 347865.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.133020 restraints weight = 363209.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.133389 restraints weight = 340061.440| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19803 Z= 0.149 Angle : 0.589 9.413 26910 Z= 0.313 Chirality : 0.046 0.449 2967 Planarity : 0.004 0.041 3459 Dihedral : 5.529 42.374 2673 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.36 % Favored : 91.55 % Rotamer: Outliers : 2.07 % Allowed : 14.88 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.39 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.17), residues: 2415 helix: -0.15 (0.27), residues: 393 sheet: -0.99 (0.19), residues: 732 loop : -1.92 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.036 0.001 TYR E 10 PHE 0.013 0.001 PHE I 351 TRP 0.025 0.001 TRP F 583 HIS 0.004 0.001 HIS I 334 Details of bonding type rmsd covalent geometry : bond 0.00351 (19761) covalent geometry : angle 0.58495 (26826) SS BOND : bond 0.00441 ( 42) SS BOND : angle 1.39665 ( 84) hydrogen bonds : bond 0.03665 ( 658) hydrogen bonds : angle 5.35149 ( 1725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.86 seconds wall clock time: 78 minutes 5.67 seconds (4685.67 seconds total)